diff --git a/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml b/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml new file mode 100644 index 00000000..3fb92fa8 --- /dev/null +++ b/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml @@ -0,0 +1,74 @@ +id: CommunityMech:000114 +name: Aerobic Denitrification Disturbance-Stable SynCom +description: A three-member aerobic denitrification SMC that maintains function under dibutyl phthalate + and levofloxacin disturbances through division of labor. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Resolve how synthetic denitrifying communities maintain functional stability under environmental + disturbances. + assembly_strategy: Pseudomonas aeruginosa N2, Acinetobacter baumannii N1, and Aeromonas hydrophila were + assembled as an aerobic denitrification SMC. + perturbation_design: Dibutyl phthalate and levofloxacin disturbance treatments. + measurement_endpoints: + - denitrification efficiency + - interspecific communication + - energy flux + - electron transfer + - EPS production + evidence: + - &id001 + reference: PMID:40020349 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Understanding how synthetic microbial community (SMC) respond to environmental disturbances + is the key to realizing SMC engineering applications. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Aerobic denitrification synthetic microbial community under pollutant disturbances. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas aeruginosa + term: + id: NCBITaxon:287 + label: Pseudomonas aeruginosa + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Acinetobacter baumannii + term: + id: NCBITaxon:470 + label: Acinetobacter baumannii + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Aeromonas hydrophila + term: + id: NCBITaxon:644 + label: Aeromonas hydrophila + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Disturbance-Stable Division of Labor + description: Members redistribute functional dominance and metabolic pathways to maintain denitrification. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Pseudomonas aeruginosa N2, Acinetobacter baumannii N1, and Aeromonas hydrophila were assembled + as an aerobic denitrification SMC. + description: Dibutyl phthalate and levofloxacin disturbance treatments. + evidence: + - *id001 diff --git a/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml b/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml new file mode 100644 index 00000000..63d660e7 --- /dev/null +++ b/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml @@ -0,0 +1,73 @@ +id: CommunityMech:000113 +name: Aerobic Denitrification Quorum-Quenching SynCom +description: A three-member aerobic denitrification SynCom whose quorum-quenching and AHL-mediated interactions + improve nitrate removal. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Improve aerobic denitrification efficiency by engineering member interactions in a synthetic + microbial community. + assembly_strategy: Acinetobacter baumannii N1, Pseudomonas aeruginosa N2, and Aeromonas hydrophila were + assembled as an SMC. + perturbation_design: Single-culture, co-culture, and three-member SMC denitrification systems were compared. + measurement_endpoints: + - nitrate reduction + - nitrite accumulation + - AHL signaling + - electron transfer + evidence: + - &id001 + reference: PMID:38277828 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: a synthetic microbial community (SMC) composed of denitrifiers Acinetobacter baumannii N1 + (AC), Pseudomonas aeruginosa N2 (PA) and Aeromonas hydrophila (AH) were constructed. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Aerobic denitrification synthetic microbial community for nitrate wastewater removal. +taxonomy: +- taxon_term: + preferred_term: Acinetobacter baumannii + term: + id: NCBITaxon:470 + label: Acinetobacter baumannii + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pseudomonas aeruginosa + term: + id: NCBITaxon:287 + label: Pseudomonas aeruginosa + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Aeromonas hydrophila + term: + id: NCBITaxon:644 + label: Aeromonas hydrophila + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: AHL-Mediated Aerobic Denitrification + description: AHL signaling and quorum quenching coordinate electron transfer and nitrate reduction. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Acinetobacter baumannii N1, Pseudomonas aeruginosa N2, and Aeromonas hydrophila were assembled + as an SMC. + description: Single-culture, co-culture, and three-member SMC denitrification systems were compared. + evidence: + - *id001 diff --git a/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml b/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml new file mode 100644 index 00000000..a29bf178 --- /dev/null +++ b/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml @@ -0,0 +1,53 @@ +id: CommunityMech:000092 +name: Arabidopsis Coumarin Root SynCom +description: A reduced Arabidopsis root-isolate SynCom used to detect rhizosphere community shifts caused + by phytoalexin, flavonoid, and coumarin exudates. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Determine how Arabidopsis specialized metabolites shape root-associated bacterial community + composition. + assembly_strategy: Reduced synthetic community of Arabidopsis thaliana root-isolated bacteria. + perturbation_design: Plant mutants deficient in secreted phytoalexins, flavonoids, and coumarins. + measurement_endpoints: + - community shifts + - rhizosphere colonization + - metabolite-dependent recruitment + evidence: + - &id001 + reference: PMID:31152139 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: We employed a reduced synthetic community (SynCom) of Arabidopsis thaliana root-isolated + bacteria to detect community shifts that occur in the absence of the secreted small-molecule phytoalexins, + flavonoids, and coumarins. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Arabidopsis root SynCom used to test plant specialized metabolite effects on rhizosphere assembly. +taxonomy: +- taxon_term: + preferred_term: Arabidopsis root-isolated bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Coumarin-Dependent Recruitment + description: Plant exuded specialized metabolites structure which bacteria persist in the rhizosphere. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Reduced synthetic community of Arabidopsis thaliana root-isolated bacteria. + description: Plant mutants deficient in secreted phytoalexins, flavonoids, and coumarins. + evidence: + - *id001 diff --git a/kb/communities/Arabidopsis_Phyllosphere_SynCom7.yaml b/kb/communities/Arabidopsis_Phyllosphere_SynCom7.yaml new file mode 100644 index 00000000..be7344ad --- /dev/null +++ b/kb/communities/Arabidopsis_Phyllosphere_SynCom7.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000091 +name: Arabidopsis Phyllosphere SynCom7 +description: A seven-strain reduced-complexity Arabidopsis phyllosphere SynCom used to test host genetic + effects on microbiota composition. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Identify Arabidopsis host genetic factors that alter phyllosphere community composition and + abundance. + assembly_strategy: Seven bacterial strains representing abundant phyllosphere phyla were inoculated + onto gnotobiotic Arabidopsis mutants. + perturbation_design: Host mutant panel affecting surface structure, cell wall, defense, secondary metabolism, + and pathogen recognition. + measurement_endpoints: + - community composition + - member abundance + - host genotype effects + evidence: + - &id001 + reference: PMID:24743269 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with + a reduced complexity synthetic bacterial community composed of seven strains representing the most + abundant phyla in the phyllosphere. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: phyllosphere + term: + id: ENVO:01001442 + label: phyllosphere + notes: Gnotobiotic Arabidopsis phyllosphere inoculated with a seven-strain bacterial community. +taxonomy: +- taxon_term: + preferred_term: Arabidopsis phyllosphere bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Host-Genotype-Structured Assembly + description: Arabidopsis host genotype shifts the abundance and composition of the phyllosphere SynCom. + interaction_type: NICHE_PARTITIONING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Seven bacterial strains representing abundant phyllosphere phyla were inoculated onto gnotobiotic + Arabidopsis mutants. + description: Host mutant panel affecting surface structure, cell wall, defense, secondary metabolism, + and pathogen recognition. + evidence: + - *id001 diff --git a/kb/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.yaml b/kb/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.yaml new file mode 100644 index 00000000..1fd1dac0 --- /dev/null +++ b/kb/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.yaml @@ -0,0 +1,65 @@ +id: CommunityMech:000118 +name: Bacillus-Bradyrhizobium Straw Humification SynCom +description: A two-member Bacillus siamensis and Bradyrhizobium japonicum SynCom that promotes maize straw + humification and soil organic carbon. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: LIGNOCELLULOSE +engineering_design: + objective: Accelerate straw humification and improve soil organic carbon through a functionally stable + SynCom. + assembly_strategy: Keystone taxa from dilution microcosms were assembled as Bacillus siamensis B and + Bradyrhizobium japonicum G. + perturbation_design: Cross-feeding assays, enzyme activity assays, and field straw-return experiments. + measurement_endpoints: + - straw humification + - soil organic carbon + - cellulase activity + - xylanase activity + - nitrogenase activity + evidence: + - &id001 + reference: PMID:41264879 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: From these taxa, we constructed a two-membered SynCom (Bacillus siamensis B and Bradyrhizobium + japonicum G). + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: soil + term: + id: ENVO:00001998 + label: soil + notes: Cropland soil receiving maize straw and two-member SynCom inoculation. +taxonomy: +- taxon_term: + preferred_term: Bacillus siamensis + term: + id: NCBITaxon:1178515 + label: Bacillus siamensis + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Bradyrhizobium japonicum + term: + id: NCBITaxon:375 + label: Bradyrhizobium japonicum + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Straw Humification Cross-Feeding + description: Bacillus and Bradyrhizobium cross-feed to promote straw-degrading enzymes and humification. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Keystone taxa from dilution microcosms were assembled as Bacillus siamensis B and Bradyrhizobium + japonicum G. + description: Cross-feeding assays, enzyme activity assays, and field straw-return experiments. + evidence: + - *id001 diff --git a/kb/communities/Banana_Fusarium_Biocontrol_SynCom12.yaml b/kb/communities/Banana_Fusarium_Biocontrol_SynCom12.yaml new file mode 100644 index 00000000..657c118c --- /dev/null +++ b/kb/communities/Banana_Fusarium_Biocontrol_SynCom12.yaml @@ -0,0 +1,74 @@ +id: CommunityMech:000095 +name: Banana Fusarium Wilt Biocontrol SynCom1.2 +description: A three-member banana rhizosphere SynCom designed for biological control of Fusarium oxysporum + f. sp. cubense tropical race 4. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Design a compatible reduced SynCom for biological control of Fusarium wilt of banana. + assembly_strategy: SynCom 1.2 combined Pseudomonas chlororaphis subsp. piscium PS5, Bacillus velezensis + BN8.2, and Trichoderma virens T2C1.4. + perturbation_design: Non-simultaneous soil application was used to reduce cross-inhibition among biocontrol + members. + measurement_endpoints: + - disease incidence + - disease severity + - antagonism against Foc TR4 + - biocontrol trait characterization + evidence: + - &id001 + reference: PMID:35992653 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'SynCom 1.2 was then designed with three isolates: Pseudomonas chlororaphis subsp. piscium + PS5, Bacillus velezensis BN8.2, and Trichoderma virens T2C1.4.' + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Banana rhizosphere-derived biological control SynCom against Fusarium wilt. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas chlororaphis + term: + id: NCBITaxon:587753 + label: Pseudomonas chlororaphis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Bacillus velezensis + term: + id: NCBITaxon:492670 + label: Bacillus velezensis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Trichoderma virens + term: + id: NCBITaxon:5547 + label: Trichoderma virens + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Coordinated Pathogen Suppression + description: Bacterial and fungal antagonists suppress Fusarium wilt while avoiding detrimental cross-inhibition. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: SynCom 1.2 combined Pseudomonas chlororaphis subsp. piscium PS5, Bacillus velezensis BN8.2, and + Trichoderma virens T2C1.4. + description: Non-simultaneous soil application was used to reduce cross-inhibition among biocontrol + members. + evidence: + - *id001 diff --git a/kb/communities/CRC_Fusobacterium_Control_SynCom.yaml b/kb/communities/CRC_Fusobacterium_Control_SynCom.yaml new file mode 100644 index 00000000..139fd6a3 --- /dev/null +++ b/kb/communities/CRC_Fusobacterium_Control_SynCom.yaml @@ -0,0 +1,59 @@ +id: CommunityMech:000126 +name: CRC Fusobacterium Control SynCom +description: A bottom-up designed seven-species synthetic microbial community for ecological control of + Fusobacterium nucleatum-associated colorectal cancer models. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Design a controllable commensal SynCom that suppresses Fusobacterium nucleatum and improves + colorectal cancer model outcomes. + assembly_strategy: Human metagenome and metabolomics data were used with metabolic network reconstruction + to design a seven-species low-competition SynCom. + perturbation_design: The SynCom was tested against Fusobacterium nucleatum in vitro and in an AOM-DSS + mouse colorectal cancer model. + measurement_endpoints: + - Fusobacterium nucleatum inhibition + - in vivo colonization + - tryptophan metabolism + - secondary bile acid conversion + - tumor inhibition + evidence: + - &id001 + reference: PMID:40433987 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: A synthetic microbial community (SynCom) is then designed by metabolic network reconstruction, + and its performance is validated using coculture experiments and an AOM-DSS induced mouse CRC model. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: colorectal gut microbiome + term: + id: UBERON:0001155 + label: colon + notes: Designed commensal SynCom validated in coculture and mouse colorectal cancer models. +taxonomy: +- taxon_term: + preferred_term: seven commensal bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Fusobacterium Ecological Suppression + description: The designed SynCom inhibits F. nucleatum growth and promotes decolonization through ecological + and metabolic control. + interaction_type: COMPETITION + evidence: + - *id001 +environmental_factors: +- name: metabolic network reconstruction design + value: A seven-species SynCom with low competitive interrelationships was designed from human metagenome + and metabolomics data. + description: The SynCom was tested against Fusobacterium nucleatum in vitro and in an AOM-DSS mouse + colorectal cancer model. + evidence: + - *id001 diff --git a/kb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml b/kb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml new file mode 100644 index 00000000..cfcd913b --- /dev/null +++ b/kb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml @@ -0,0 +1,86 @@ +id: CommunityMech:000087 +name: Cellulose-to-Methane Quad-Culture SynCom +description: A four-species anaerobic synthetic community coupling cellulose degradation, sulfate reduction, + and methanogenesis. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: METHANOGENESIS +engineering_design: + objective: Resolve higher-order cross-feeding, competition, and synergy during anaerobic conversion + of cellulose to methane and carbon dioxide. + assembly_strategy: Rational functional-guild assembly of cellulolytic, sulfate-reducing, hydrogenotrophic + methanogenic, and acetoclastic methanogenic members. + perturbation_design: Control cultures were compared with sulfate addition using metaproteomics, metabolite + profiling, and stoichiometric modeling. + measurement_endpoints: + - methane production + - cellulose degradation + - sulfate reduction + - cross-feeding fluxes + evidence: + - &id001 + reference: PMID:36847519 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here, we constructed a quad-culture consisting of a cellulolytic bacterium (Ruminiclostridium + cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic methanogen + (Methanosaeta concilii), and a sulfate-reducing bacterium (Desulfovibrio vulgaris). + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Anaerobic cellulose-degrading laboratory quad-culture with sulfate perturbation. +taxonomy: +- taxon_term: + preferred_term: Ruminiclostridium cellulolyticum + term: + id: NCBITaxon:1521 + label: Clostridium cellulolyticum + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Methanospirillum hungatei + term: + id: NCBITaxon:323259 + label: Methanospirillum hungatei + functional_role: + - SYNTROPHIC_PARTNER + evidence: + - *id001 +- taxon_term: + preferred_term: Methanosaeta concilii + term: + id: NCBITaxon:2224 + label: Methanosaeta concilii + functional_role: + - SYNTROPHIC_PARTNER + evidence: + - *id001 +- taxon_term: + preferred_term: Desulfovibrio vulgaris + term: + id: NCBITaxon:881 + label: Desulfovibrio vulgaris + functional_role: + - SYNTROPHIC_PARTNER + evidence: + - *id001 +ecological_interactions: +- name: Cellulose Cross-Feeding to Methane + description: Cellulose fermentation products are exchanged with methanogens and sulfate reducers, producing + methane and modulating competition. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Rational functional-guild assembly of cellulolytic, sulfate-reducing, hydrogenotrophic methanogenic, + and acetoclastic methanogenic members. + description: Control cultures were compared with sulfate addition using metaproteomics, metabolite profiling, + and stoichiometric modeling. + evidence: + - *id001 diff --git a/kb/communities/Defined_Multispecies_Enamel_Caries_Model.yaml b/kb/communities/Defined_Multispecies_Enamel_Caries_Model.yaml new file mode 100644 index 00000000..7dd5b02d --- /dev/null +++ b/kb/communities/Defined_Multispecies_Enamel_Caries_Model.yaml @@ -0,0 +1,144 @@ +id: CommunityMech:000080 +name: Defined Multispecies Enamel Caries Model +description: >- + A defined four-member oral biofilm model for in vitro enamel caries + development, composed of Lactobacillus casei, Streptococcus mutans, + Streptococcus salivarius, and Streptococcus sanguinis on + salivary-pellicle-coated enamel slabs. The system was used to quantify how + sucrose, fluoride, and calcium shift biofilm growth and enamel + demineralization. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: >- + Build a defined multispecies enamel caries model that reports dose-dependent + effects of sucrose, fluoride, and calcium on biofilm growth and enamel + demineralization. + assembly_strategy: >- + Bottom-up assembly of four oral species on salivary-pellicle-coated enamel + slabs with daily medium replacement over a four-day biofilm growth period. + perturbation_design: >- + Medium sucrose concentration was varied between 0.5 and 1.0%, fluoride + between 0.4 and 1.0 ppm, and calcium between 1.0 and 2.0 mM. + measurement_endpoints: + - Viable cell counts + - Surface microhardness change + - Lesion depth + - Integrated mineral loss + evidence: + - reference: PMID:23446436 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Defined-multispecies biofilms, formed by Lactobacillus casei, + Streptococcus mutans, S. salivarius and S. sanguinis, were grown on the + surface of salivary-pellicle-coated enamel slabs + explanation: Supports the member composition and cultivation platform of the model. +environment_term: + preferred_term: cariogenic enamel biofilm on tooth surface + term: + id: ENVO:01001034 + label: environment determined by a biofilm on an animal surface + notes: >- + In vitro enamel caries system using salivary-pellicle-coated enamel slabs + as the colonization surface. +taxonomy: +- taxon_term: + preferred_term: Lactobacillus casei + term: + id: NCBITaxon:1582 + label: Lacticaseibacillus casei + notes: Study uses the historical name Lactobacillus casei. + evidence: + - reference: PMID:23446436 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Defined-multispecies biofilms, formed by Lactobacillus casei, + Streptococcus mutans, S. salivarius and S. sanguinis, were grown on the + surface of salivary-pellicle-coated enamel slabs + explanation: Documents Lactobacillus casei as a member of the enamel caries consortium. +- taxon_term: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + evidence: + - reference: PMID:23446436 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Defined-multispecies biofilms, formed by Lactobacillus casei, + Streptococcus mutans, S. salivarius and S. sanguinis, were grown on the + surface of salivary-pellicle-coated enamel slabs + explanation: Documents Streptococcus mutans as a member of the enamel caries consortium. +- taxon_term: + preferred_term: Streptococcus salivarius + term: + id: NCBITaxon:1304 + label: Streptococcus salivarius + evidence: + - reference: PMID:23446436 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Defined-multispecies biofilms, formed by Lactobacillus casei, + Streptococcus mutans, S. salivarius and S. sanguinis, were grown on the + surface of salivary-pellicle-coated enamel slabs + explanation: Documents Streptococcus salivarius as a member of the enamel caries consortium. +- taxon_term: + preferred_term: Streptococcus sanguinis + term: + id: NCBITaxon:1305 + label: Streptococcus sanguinis + evidence: + - reference: PMID:23446436 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Defined-multispecies biofilms, formed by Lactobacillus casei, + Streptococcus mutans, S. salivarius and S. sanguinis, were grown on the + surface of salivary-pellicle-coated enamel slabs + explanation: Documents Streptococcus sanguinis as a member of the enamel caries consortium. +environmental_factors: +- name: Sucrose concentration + value: 0.5-1.0 + unit: '%' + description: >- + Sucrose was titrated to test how carbohydrate supply alters multispecies + growth and enamel demineralization. + evidence: + - reference: PMID:23446436 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + The aims of this study were to describe and validate an in vitro + multispecies microbial biofilm model for caries development by evaluating + the effects of varying medium concentration of sucrose (0.5 and 1.0%) + explanation: Documents the sucrose range used in the enamel caries model. +- name: Fluoride concentration + value: 0.4-1.0 + unit: ppm + description: Fluoride was varied to quantify inhibition of biofilm-driven enamel caries. + evidence: + - reference: PMID:23446436 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + There was a decrease in %SMC in response to increased fluoride and + calcium concentrations (p < 0.001). Lower IML (p < 0.001) and LD (p < + 0.05) were found in the presence of 0.8 and 1.0 ppm F. + explanation: Supports fluoride-dependent attenuation of enamel demineralization. +- name: Calcium concentration + value: 1.0-2.0 + unit: mM + description: Calcium supplementation was varied to test its effect on caries inhibition. + evidence: + - reference: PMID:23446436 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + There was a decrease in %SMC in response to increased fluoride and + calcium concentrations (p < 0.001). + explanation: Supports calcium as a controlled environmental factor in the model. diff --git a/kb/communities/Desert_Tomato_Salt_Stress_SynCom5.yaml b/kb/communities/Desert_Tomato_Salt_Stress_SynCom5.yaml new file mode 100644 index 00000000..525931ff --- /dev/null +++ b/kb/communities/Desert_Tomato_Salt_Stress_SynCom5.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000094 +name: Desert-Derived Tomato Salt Stress SynCom5 +description: A five-member desert-root bacterial SynCom that protects tomato plants from high salt stress + in non-sterile soil. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Engineer a simplified desert microbiome SynCom that confers abiotic salt-stress resilience + to tomato. + assembly_strategy: Five bacterial strains originating from the root of Indigofera argentea were assembled + into a SynCom. + perturbation_design: High salt stress in natural non-sterile soil substrate. + measurement_endpoints: + - tomato salt-stress resilience + - SynCom strain penetrance + - salt-stress gene expression + - ion accumulation + evidence: + - &id001 + reference: PMID:35444261 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here we show that a SynCom of five bacterial strains, originating from the root of the desert + plant Indigofera argentea, protected tomato plants growing in a non-sterile substrate against a + high salt stress. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Five bacterial strains from desert plant roots applied to tomato in non-sterile substrate. +taxonomy: +- taxon_term: + preferred_term: desert root bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Desert Microbiome Salt Protection + description: Desert root isolates improve tomato salt-stress tolerance in a natural soil microbiome + context. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Five bacterial strains originating from the root of Indigofera argentea were assembled into a + SynCom. + description: High salt stress in natural non-sterile soil substrate. + evidence: + - *id001 diff --git a/kb/communities/Early_Dental_Biofilm_FiveSpecies.yaml b/kb/communities/Early_Dental_Biofilm_FiveSpecies.yaml new file mode 100644 index 00000000..35f62001 --- /dev/null +++ b/kb/communities/Early_Dental_Biofilm_FiveSpecies.yaml @@ -0,0 +1,142 @@ +id: CommunityMech:000081 +name: Early Dental Biofilm Five-Species Model +description: >- + A defined five-member oral biofilm model representing early acidogenic stages + of the caries process. The community combines Streptococcus oralis, + Streptococcus sanguinis, Streptococcus mitis, Streptococcus downei, and + Actinomyces naeslundii in flow-channel biofilms to reproduce the composition, + architecture, and microscale pH heterogeneity of early dental plaque. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: >- + Model early acidogenic dental plaque and resolve extracellular pH + microenvironments during glucose challenge. + assembly_strategy: >- + Bottom-up assembly of five oral isolates selected to mimic the bacterial + community present during early acidogenic stages of caries. + perturbation_design: >- + Biofilms were grown in flow channels and challenged with salivary + solutions containing glucose for time-resolved pH imaging at the + biofilm-substrate interface. + measurement_endpoints: + - Fluorescence in situ hybridization + - Confocal laser scanning microscopy + - Real-time extracellular pH imaging + evidence: + - reference: PMID:21966490 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + In this study, we designed a laboratory biofilm model that mimics the + bacterial community present during early acidogenic stages of the caries + process. + explanation: Supports the purpose and composition rationale of the model. +environment_term: + preferred_term: dental plaque biofilm on tooth surface + term: + id: ENVO:01001034 + label: environment determined by a biofilm on an animal surface + notes: >- + Flow-channel dental biofilm model built to emulate early supragingival + plaque under salivary glucose challenge. +taxonomy: +- taxon_term: + preferred_term: Streptococcus oralis + term: + id: NCBITaxon:1303 + label: Streptococcus oralis + evidence: + - reference: PMID:21966490 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Strains of Streptococcus oralis, Streptococcus sanguinis, Streptococcus + mitis, Streptococcus downei and Actinomyces naeslundii were employed in + the model. + explanation: Documents Streptococcus oralis as a member of the five-species model. +- taxon_term: + preferred_term: Streptococcus sanguinis + term: + id: NCBITaxon:1305 + label: Streptococcus sanguinis + evidence: + - reference: PMID:21966490 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Strains of Streptococcus oralis, Streptococcus sanguinis, Streptococcus + mitis, Streptococcus downei and Actinomyces naeslundii were employed in + the model. + explanation: Documents Streptococcus sanguinis as a member of the five-species model. +- taxon_term: + preferred_term: Streptococcus mitis + term: + id: NCBITaxon:28037 + label: Streptococcus mitis + evidence: + - reference: PMID:21966490 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Strains of Streptococcus oralis, Streptococcus sanguinis, Streptococcus + mitis, Streptococcus downei and Actinomyces naeslundii were employed in + the model. + explanation: Documents Streptococcus mitis as a member of the five-species model. +- taxon_term: + preferred_term: Streptococcus downei + term: + id: NCBITaxon:1317 + label: Streptococcus downei + evidence: + - reference: PMID:21966490 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Strains of Streptococcus oralis, Streptococcus sanguinis, Streptococcus + mitis, Streptococcus downei and Actinomyces naeslundii were employed in + the model. + explanation: Documents Streptococcus downei as a member of the five-species model. +- taxon_term: + preferred_term: Actinomyces naeslundii + term: + id: NCBITaxon:1655 + label: Actinomyces naeslundii + evidence: + - reference: PMID:21966490 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Strains of Streptococcus oralis, Streptococcus sanguinis, Streptococcus + mitis, Streptococcus downei and Actinomyces naeslundii were employed in + the model. + explanation: Documents Actinomyces naeslundii as a member of the five-species model. +environmental_factors: +- name: Glucose challenge + description: >- + Salivary solutions containing glucose were used to trigger anaerobic + glycolysis and map extracellular pH at the biofilm-substrate interface. + evidence: + - reference: PMID:21966490 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + We employed the pH-sensitive ratiometric probe C-SNARF-4 to perform + real-time microscopic analyses of the biofilm pH in response to salivary + solutions containing glucose. + explanation: Documents the carbohydrate perturbation used to probe pH dynamics. +- name: Persistent acidic microenvironments + description: >- + Anaerobic glycolysis generated conserved extracellular acidic microniches + across the developing biofilm. + evidence: + - reference: PMID:21966490 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: >- + Anaerobic glycolysis in the model biofilms created a mildly acidic + environment. Decrease in pH in different areas of the biofilms varied, + and distinct extracellular pH-microenvironments were conserved over + several hours. + explanation: Supports the dysbiosis-relevant pH heterogeneity captured by the model. diff --git a/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml b/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml new file mode 100644 index 00000000..81244fee --- /dev/null +++ b/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000089 +name: GLBRC Exometabolite Transwell SynCom System +description: A synthetic community assay system for probing chemically mediated microbial interactions + through shared exometabolites. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOTECHNOLOGY +engineering_design: + objective: Interrogate exometabolite interactions among physically separated microbial populations. + assembly_strategy: Synthetic community members are cultured in a filter plate system that separates + cells while allowing chemical exchange through shared medium. + perturbation_design: Shared-reservoir chemical interactions are assayed using sensitive mass spectrometry. + measurement_endpoints: + - exometabolite profiles + - member growth + - productivity + - gene regulation + evidence: + - &id001 + reference: PMID:29152587 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we describe a straightforward synthetic community system that can be used to interrogate + exometabolite interactions among microorganisms. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Filter plate Transwell synthetic community system for exometabolite-mediated microbial interactions. +taxonomy: +- taxon_term: + preferred_term: exometabolite-interacting bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Exometabolite-Mediated Interaction + description: Community members interact chemically through small molecules, extracellular enzymes, and + antibiotics in shared medium. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Synthetic community members are cultured in a filter plate system that separates cells while + allowing chemical exchange through shared medium. + description: Shared-reservoir chemical interactions are assayed using sensitive mass spectrometry. + evidence: + - *id001 diff --git a/kb/communities/Garlic_Pseudomonas_SynCom6.yaml b/kb/communities/Garlic_Pseudomonas_SynCom6.yaml new file mode 100644 index 00000000..1a706d57 --- /dev/null +++ b/kb/communities/Garlic_Pseudomonas_SynCom6.yaml @@ -0,0 +1,53 @@ +id: CommunityMech:000093 +name: Garlic Rhizosphere Pseudomonas SynCom6 +description: A six-strain Pseudomonas SynCom selected from garlic rhizosphere microbiome data for plant + growth promotion. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Use top-down rhizosphere microbiome analysis to identify and apply plant growth-promoting + Pseudomonas strains. + assembly_strategy: Six Pseudomonas strains isolated from garlic rhizosphere were combined into a SynCom. + perturbation_design: Garlic growth periods, soil types, and agricultural practices informed candidate + selection. + measurement_endpoints: + - plant growth promotion + - PGPR enrichment + - rhizosphere community structure + evidence: + - &id001 + reference: PMID:32762153 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: SynCom with six Pseudomonas strains isolated from the garlic rhizosphere were constructed, + which showed that they have the ability to promote plant growth. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Six Pseudomonas strains isolated from the garlic rhizosphere. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Pseudomonas-Mediated Growth Promotion + description: Pseudomonas strains selected from garlic rhizosphere promote host plant growth. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Six Pseudomonas strains isolated from garlic rhizosphere were combined into a SynCom. + description: Garlic growth periods, soil types, and agricultural practices informed candidate selection. + evidence: + - *id001 diff --git a/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml b/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml new file mode 100644 index 00000000..4e4c6bcf --- /dev/null +++ b/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml @@ -0,0 +1,58 @@ +id: CommunityMech:000122 +name: Honeybee Core-20 Defined Microbiota +description: A stably transmitted 20-strain synthetic gut microbiota from honeybee intestine that primes + host immunity and reduces Hafnia alvei prevalence. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Test whether a defined honeybee gut community can stably colonize and protect the host against + pathogen prevalence. + assembly_strategy: Twenty strains isolated from honeybee intestine were selected using phylogeny analysis + to create the Core-20 community. + perturbation_design: Honeybees were colonized through passages and challenged in the context of Hafnia + alvei inhibition. + measurement_endpoints: + - immune gene expression + - Hafnia alvei prevalence + - stable gut colonization + - carbohydrate-utilization functions + evidence: + - &id001 + reference: PMID:36532452 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: we assembled a defined microbial community based on phylogeny analysis, the 'Core-20' community, + consisting of 20 strains isolated from the honeybee intestine. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: honeybee intestine + term: + id: UBERON:0000160 + label: intestine + notes: Defined microbial community isolated from the honeybee gut. +taxonomy: +- taxon_term: + preferred_term: honeybee gut bacterial Core-20 members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Immune-Mediated Pathogen Protection + description: The defined Core-20 community primes host immune gene expression and reduces Hafnia alvei + prevalence. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: stably transmitted defined microbiota + value: The Core-20 community was passaged through honeybee guts and evaluated for stable colonization + and immune effects. + description: Honeybees were colonized through passages and challenged in the context of Hafnia alvei + inhibition. + evidence: + - *id001 diff --git a/kb/communities/Jala_Maize_PGPB_SynCom.yaml b/kb/communities/Jala_Maize_PGPB_SynCom.yaml new file mode 100644 index 00000000..7b69e445 --- /dev/null +++ b/kb/communities/Jala_Maize_PGPB_SynCom.yaml @@ -0,0 +1,81 @@ +id: CommunityMech:000097 +name: Jala Maize PGPB SynCom +description: Synthetic microbial communities assembled from plant growth-promoting bacteria of the Jala + maize landrace to improve Zea mays growth and yield. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Promote maize growth and yield using PGPB SynComs from native maize landrace isolates. + assembly_strategy: Multiple SynComs were assembled from PGPB with growth promotion, biocontrol, and + induced systemic resistance traits. + perturbation_design: Gnotobiotic, greenhouse, and open-field maize experiments. + measurement_endpoints: + - root length + - shoot length + - greenhouse growth + - field yield + evidence: + - &id001 + reference: PMID:37275168 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: synthetic microbial communities (SynCom) were assembled with a set of PGPB isolated from + the Jala maize landrace + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Plant growth-promoting bacteria isolated from Jala maize landrace. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas protegens + term: + id: NCBITaxon:380021 + label: Pseudomonas protegens + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pantoea ananatis + term: + id: NCBITaxon:553 + label: Pantoea ananatis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Klebsiella variicola + term: + id: NCBITaxon:244366 + label: Klebsiella variicola + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Burkholderia sp. + term: + id: NCBITaxon:32008 + label: Burkholderia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Maize Growth Promotion + description: PGPB members contribute growth-promotion, biocontrol, and induced systemic resistance traits. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Multiple SynComs were assembled from PGPB with growth promotion, biocontrol, and induced systemic + resistance traits. + description: Gnotobiotic, greenhouse, and open-field maize experiments. + evidence: + - *id001 diff --git a/kb/communities/LBNL_Brachypodium_Drought_SynCom15.yaml b/kb/communities/LBNL_Brachypodium_Drought_SynCom15.yaml new file mode 100644 index 00000000..42490a02 --- /dev/null +++ b/kb/communities/LBNL_Brachypodium_Drought_SynCom15.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000086 +name: LBNL Brachypodium Drought SynCom15 +description: A stable 15-member Brachypodium rhizosphere SynCom constructed with network and cultivation-guided + methods to promote drought resilience. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Construct a stable trait-informed bacterial SynCom that improves Brachypodium performance + under drought stress. + assembly_strategy: Network analysis and cultivation-guided selection of 15 rhizobiome strains spanning + five bacterial phyla. + perturbation_design: Drought stress and in vitro versus in planta stability testing. + measurement_endpoints: + - SynCom stability + - plant recovery from drought + - root-tip colonization + - plant growth-promoting traits + evidence: + - &id001 + reference: PMID:40862137 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here, we present a systematic approach using a combination of network analysis and cultivation-guided + methods to construct a 15-member SynCom from the rhizobiome of Brachypodium distachyon. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Fifteen-member Brachypodium distachyon rhizobiome SynCom tested under drought stress. +taxonomy: +- taxon_term: + preferred_term: Brachypodium rhizobiome bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Drought Resilience Promotion + description: SynCom members encode and express plant growth-promoting traits linked to drought recovery. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Network analysis and cultivation-guided selection of 15 rhizobiome strains spanning five bacterial + phyla. + description: Drought stress and in vitro versus in planta stability testing. + evidence: + - *id001 diff --git a/kb/communities/LBNL_Human_Gut_Interaction_SynCom.yaml b/kb/communities/LBNL_Human_Gut_Interaction_SynCom.yaml new file mode 100644 index 00000000..c5db6fe0 --- /dev/null +++ b/kb/communities/LBNL_Human_Gut_Interaction_SynCom.yaml @@ -0,0 +1,56 @@ +id: CommunityMech:000120 +name: LBNL Human Gut Interaction SynCom +description: A diverse synthetic human gut microbiome community used with model-guided time-series experiments + to infer pairwise ecological interactions and metabolic drivers of coexistence. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Infer ecological interaction structure and metabolic design principles in a synthetic human + gut microbiome community. + assembly_strategy: Defined human gut species were assembled into lower-order and higher-order consortia + for time-resolved community measurements. + perturbation_design: Initial species proportions and lower-order community combinations were varied + to predict higher-dimensional dynamics. + measurement_endpoints: + - time-resolved abundance dynamics + - ecological interaction network + - extracellular metabolites + - coexistence stability + evidence: + - &id001 + reference: PMID:29930200 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This method was employed to decipher microbial interactions in a diverse human gut microbiome + synthetic community. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: human gut microbiome + term: + id: UBERON:0001007 + label: digestive system + notes: Synthetic human-associated intestinal community studied in vitro. +taxonomy: +- taxon_term: + preferred_term: human gut bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Pairwise Gut Community Interactions + description: Pairwise positive and negative interactions structure multi-species community dynamics. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: model-guided synthetic community design + value: Lower-order assemblages were used to predict higher-dimensional human gut SynCom dynamics. + description: Initial species proportions and lower-order community combinations were varied to predict + higher-dimensional dynamics. + evidence: + - *id001 diff --git a/kb/communities/LBNL_Switchgrass_Soil_SynCom16.yaml b/kb/communities/LBNL_Switchgrass_Soil_SynCom16.yaml new file mode 100644 index 00000000..02efef69 --- /dev/null +++ b/kb/communities/LBNL_Switchgrass_Soil_SynCom16.yaml @@ -0,0 +1,58 @@ +id: CommunityMech:000085 +name: LBNL Switchgrass Soil SynCom16 +description: A 16-member synthetic soil community from switchgrass-associated soil, optimized for reproducible + in vitro and EcoFAB plant-microbe experiments. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Provide a reproducible, tunable model soil SynCom for plant-soil microbe interaction studies. + assembly_strategy: Bottom-up assembly of 16 culturable soil microorganisms commonly found in plant rhizospheres, + with tuned inoculum ratios and cryopreservation. + perturbation_design: Low-nutrient media, starting composition ratios, cryopreservation, and EcoFAB plant + colonization were evaluated. + measurement_endpoints: + - community alpha diversity + - replicate reproducibility + - cryopreservation recovery + - EcoFAB colonization + evidence: + - &id001 + reference: PMID:36472419 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the + rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, + has been developed and optimized for in vitro experiments. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: soil + term: + id: ENVO:00001998 + label: soil + notes: Sixteen soil microorganisms isolated from soil surrounding switchgrass were optimized as a reproducible + rhizosphere SynCom. +taxonomy: +- taxon_term: + preferred_term: soil bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Reproducible Rhizosphere Assembly + description: Defined members reproducibly assemble under low-nutrient and EcoFAB conditions. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Bottom-up assembly of 16 culturable soil microorganisms commonly found in plant rhizospheres, + with tuned inoculum ratios and cryopreservation. + description: Low-nutrient media, starting composition ratios, cryopreservation, and EcoFAB plant colonization + were evaluated. + evidence: + - *id001 diff --git a/kb/communities/MSC2_Model_Soil_Consortium.yaml b/kb/communities/MSC2_Model_Soil_Consortium.yaml new file mode 100644 index 00000000..c30df366 --- /dev/null +++ b/kb/communities/MSC2_Model_Soil_Consortium.yaml @@ -0,0 +1,208 @@ +id: CommunityMech:000079 +name: Model Soil Consortium-2 (MSC-2) +description: >- + Reduced-complexity model soil consortium assembled from MSC-1 isolates to study + community-level chitin decomposition, interspecies interactions, and emergent + phenotypes in soil. MSC-2 contains eight bacterial members spanning diverse phyla + and was used for isolate genome sequencing, 16S profiling, metatranscriptomics, + metabolomics, and KBase-enabled metabolic modeling in the Hofmockel Soil Microbiome + SFA context. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: >- + Build a reduced, tractable soil consortium for studying how community context + shapes chitin degradation and member success during decomposition. + assembly_strategy: >- + Eight isolates were selected from MSC-1 to include both chitin degraders and + nondegraders while maximizing taxonomic diversity. + inoculation_strategy: Eight individually isolated strains assembled into a defined mixed community. + passaging_regimen: >- + Developed as a reduced-complexity follow-on to the naturally evolved MSC-1 soil + consortium for monoculture and coculture chitin assays. + measurement_endpoints: + - isolate growth on chitin and alternative carbon sources + - 16S rRNA community composition profiling + - metatranscriptomics during community growth on chitin + - community metabolomics during chitin decomposition + notes: >- + The KBase Soil Microbiome SFA page describes MSC-2 as one of the model consortia + used for OMEGGA and ModelSEED2 workflows. + evidence: + - reference: PMID:36154140 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'Chitin was applied to a model soil consortium that we developed, "model soil consortium-2" (MSC-2), consisting of eight members of diverse phyla and including both chitin degraders and nondegraders.' + explanation: Supports the reduced eight-member MSC-2 design and mixed degrader/nondegrader composition. +environment_term: + preferred_term: grassland soil + term: + id: ENVO:00001998 + label: soil + notes: Isolates were derived from IAREC grassland soil in Prosser, Washington. +taxonomy: +- taxon_term: + preferred_term: Streptomyces sp. MSC1_001 + term: + id: NCBITaxon:1931 + label: Streptomyces sp. + strain_designation: + strain_name: MSC1_001 + genome_accession: GCA_023667545.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667545.1 + functional_role: + - CROSS_FEEDER +- taxon_term: + preferred_term: Neorhizobium tomejilense MSC1_005 + term: + id: NCBITaxon:2093828 + label: Neorhizobium tomejilense + strain_designation: + strain_name: MSC1_005 + genome_accession: GCA_023667605.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667605.1 + functional_role: + - CROSS_FEEDER +- taxon_term: + preferred_term: Dyadobacter sp. MSC1_007 + term: + id: NCBITaxon:1914288 + label: Dyadobacter sp. + strain_designation: + strain_name: MSC1_007 + genome_accession: GCA_023667495.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667495.1 + functional_role: + - PRIMARY_DEGRADER +- taxon_term: + preferred_term: Sphingopyxis sp. MSC1_008 + term: + id: NCBITaxon:1908224 + label: Sphingopyxis sp. + strain_designation: + strain_name: MSC1_008 + genome_accession: GCA_023197165.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023197165.1 + functional_role: + - CROSS_FEEDER +- taxon_term: + preferred_term: Ensifer adhaerens MSC1_011 + term: + id: NCBITaxon:106592 + label: Ensifer adhaerens + strain_designation: + strain_name: MSC1_011 + genome_accession: GCA_023667555.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667555.1 + functional_role: + - PRIMARY_DEGRADER +- taxon_term: + preferred_term: Variovorax beijingensis MSC1_012 + term: + id: NCBITaxon:2496117 + label: Variovorax beijingensis + strain_designation: + strain_name: MSC1_012 + genome_accession: GCA_023667525.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667525.1 + functional_role: + - PRIMARY_DEGRADER + - CROSS_FEEDER +- taxon_term: + preferred_term: Sinorhizobium meliloti MSC1_014 + term: + id: NCBITaxon:382 + label: Sinorhizobium meliloti + strain_designation: + strain_name: MSC1_014 + genome_accession: GCA_023197145.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023197145.1 + functional_role: + - PRIMARY_DEGRADER +- taxon_term: + preferred_term: Rhodococcus sp. MSC1_016 + term: + id: NCBITaxon:1827 + label: Rhodococcus + strain_designation: + strain_name: MSC1_016 + genome_accession: GCA_023667485.1 + genome_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_023667485.1 + functional_role: + - PRIMARY_DEGRADER +associated_datasets: +- name: MSC-2 isolate genomes + dataset_type: GENOME + repository: NCBI_BIOPROJECT + accession: PRJNA788902 + url: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA788902 + description: BioProject containing the eight isolate genome assemblies used for MSC-2. +- name: MSC-2 bacterial isolate genomes (PNNL DataHub) + dataset_type: GENOME + repository: OTHER + accession: 10.25584/PNNLDH/1986536 + url: https://data.pnnl.gov/group/nodes/dataset/33234 + description: PNNL DataHub record linking the MSC-2 isolate genome assemblies and accessions. +- name: MSC-2 16S growth dataset + dataset_type: AMPLICON_16S + repository: OTHER + accession: PNNLDH:33231 + url: https://data.pnnl.gov/group/nodes/dataset/33231 + description: 16S rRNA gene data from MSC-2 growth experiments. +- name: MSC-2 metatranscriptomic dataset + dataset_type: METATRANSCRIPTOME + repository: OTHER + accession: PNNLDH:33232 + url: https://data.pnnl.gov/group/nodes/dataset/33232 + description: Metatranscriptomic data from MSC-2 chitin growth assays. +- name: MSC-2 primary publication + dataset_type: OTHER + repository: OTHER + accession: PMID:36154140 + url: https://pubmed.ncbi.nlm.nih.gov/36154140/ + description: Primary publication describing MSC-2 assembly, multiomics, and community interaction results. +ecological_interactions: +- name: Chitin Breakdown Product Sharing + description: >- + Community growth on chitin is supported by interspecies sharing of decomposition + products, so the most abundant members are not necessarily the taxa that directly + metabolize chitin in monoculture. + interaction_type: CROSS_FEEDING + metabolites: + - preferred_term: chitin + term: + id: CHEBI:18246 + label: chitin + downstream: + - target: Community growth on chitin decomposition products + evidence: + - reference: PMID:36154140 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the most abundant members of MSC-2 were not those that were able to metabolize chitin itself, but rather those that were able to take full advantage of interspecies interactions to grow on chitin decomposition products + explanation: Supports cross-feeding and shared access to products released during community chitin degradation. +- name: Community-Responsive Streptomyces Chitin Phenotype + description: >- + Streptomyces exhibits a community-responsive chitin phenotype, and MSC-2 organizes + members into distinct functional roles during decomposition. + interaction_type: NICHE_PARTITIONING + source_taxon: + preferred_term: Streptomyces sp. MSC1_001 + term: + id: NCBITaxon:1931 + label: Streptomyces sp. + downstream: + - target: Distinct functional roles during chitin degradation + evidence: + - reference: PMID:36154140 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Emergent properties of both species and the community were found, including changes in the chitin degradation potential of Streptomyces species and organization of all species into distinct roles in the chitin degradation process. + explanation: Supports that Streptomyces behavior and community roles depend on the surrounding MSC-2 membership. +external_resources: +- name: KBase Soil Microbiome SFA collaboration page + repository: KBASE + resource_id: hofmockel-sfa + url: https://www.kbase.us/research/hofmockel-sfa/ + description: KBase Soil Microbiome SFA page describing OMEGGA and MSC-2 use in ModelSEED2 workflows. diff --git a/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml b/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml new file mode 100644 index 00000000..60741e68 --- /dev/null +++ b/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml @@ -0,0 +1,54 @@ +id: CommunityMech:000099 +name: Maize Benzoxazinoid-Metabolizing SynComs +description: Two maize root bacterial SynComs sharing six common strains and differing in a seventh benzoxazinoid-metabolizing + member. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Test how individual benzoxazinoid tolerance and metabolism traits combine at community scale. + assembly_strategy: Two seven-strain synthetic communities of maize root bacteria with shared core strains + and alternate benzoxazinoid-metabolizing capacity. + perturbation_design: In vitro exposure to MBOA, a maize benzoxazinoid breakdown product. + measurement_endpoints: + - benzoxazinoid metabolization + - community composition + - strain interactions + evidence: + - &id001 + reference: PMID:40853002 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we designed two synthetic communities of maize root bacteria that share six common strains + and differ in their ability to metabolize benzoxazinoids based on the seventh strain. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Maize root bacterial synthetic communities exposed to benzoxazinoid exudates. +taxonomy: +- taxon_term: + preferred_term: maize root bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Benzoxazinoid-Mediated Niche Partitioning + description: Community members differ in benzoxazinoid tolerance and metabolism, redirecting metabolite + fate. + interaction_type: NICHE_PARTITIONING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Two seven-strain synthetic communities of maize root bacteria with shared core strains and alternate + benzoxazinoid-metabolizing capacity. + description: In vitro exposure to MBOA, a maize benzoxazinoid breakdown product. + evidence: + - *id001 diff --git a/kb/communities/Maize_Drought_Response_SynCom.yaml b/kb/communities/Maize_Drought_Response_SynCom.yaml new file mode 100644 index 00000000..32c7f5f8 --- /dev/null +++ b/kb/communities/Maize_Drought_Response_SynCom.yaml @@ -0,0 +1,56 @@ +id: CommunityMech:000101 +name: Maize Drought Response SynCom +description: A plant-beneficial bacterial SynCom that modulates physiology and drought response of commercial + maize hybrids. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Quantify how bacterial SynCom inoculation changes maize physiology, resilience, and productivity + under drought. + assembly_strategy: Synthetic community of plant-beneficial bacteria applied to three commercial maize + hybrids. + perturbation_design: Drought stress and rehydration tracked with real-time non-invasive phenotyping. + measurement_endpoints: + - yield loss + - leaf temperature + - turgor loss + - sap flow + - SynCom colonization + evidence: + - &id001 + reference: PMID:34745050 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we used a non-invasive real-time phenotyping platform in a one-to-one (plant-sensors) set + up to investigate the impact of a synthetic community (SynCom) harboring plant-beneficial bacteria + on the physiology and response of three commercial maize hybrids to drought stress (DS). + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Plant-beneficial bacterial SynCom applied to maize under drought stress. +taxonomy: +- taxon_term: + preferred_term: plant-beneficial maize bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Maize Drought Physiology Modulation + description: SynCom inoculation modulates maize water-use physiology and drought recovery. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Synthetic community of plant-beneficial bacteria applied to three commercial maize hybrids. + description: Drought stress and rehydration tracked with real-time non-invasive phenotyping. + evidence: + - *id001 diff --git a/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml b/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml new file mode 100644 index 00000000..91af733e --- /dev/null +++ b/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml @@ -0,0 +1,65 @@ +id: CommunityMech:000106 +name: Medicago Nodule Biofertilizer SynCom +description: A four-strain nodule synthetic bacterial community with Ensifer and Pseudomonas members for + Medicago sativa biofertilization under abiotic stress. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Promote alfalfa growth and nodulation in degraded estuarine soils under metal, salinity, + drought, and heat stress. + assembly_strategy: Two Ensifer and two Pseudomonas strains isolated from Medicago nodules were assembled + as a SynCom. + perturbation_design: Metal contamination, salinity, drought, and high temperature in estuarine soils. + measurement_endpoints: + - plant growth + - nodulation + - PGP trait maintenance + - abiotic stress tolerance + evidence: + - &id001 + reference: PMID:37299063 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This work was aimed to determine the potential of a nodule synthetic bacterial community + (SynCom), including two Ensifer sp. and two Pseudomonas sp. strains isolated from Medicago spp. + nodules, to promote M. sativa growth and nodulation in degraded estuarine soils under several abiotic + stresses + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: soil + term: + id: ENVO:00001998 + label: soil + notes: Estuarine soils inoculated with Medicago nodule-derived bacteria. +taxonomy: +- taxon_term: + preferred_term: Ensifer sp. + term: + id: NCBITaxon:106591 + label: Ensifer + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Legume Nodule Biofertilization + description: Nodule endophytes support growth and nodulation under abiotic stress. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Two Ensifer and two Pseudomonas strains isolated from Medicago nodules were assembled as a SynCom. + description: Metal contamination, salinity, drought, and high temperature in estuarine soils. + evidence: + - *id001 diff --git a/kb/communities/Methane_Oxidation_CrVI_Reduction_SynCom.yaml b/kb/communities/Methane_Oxidation_CrVI_Reduction_SynCom.yaml new file mode 100644 index 00000000..0df39c13 --- /dev/null +++ b/kb/communities/Methane_Oxidation_CrVI_Reduction_SynCom.yaml @@ -0,0 +1,73 @@ +id: CommunityMech:000119 +name: Methane Oxidation-Cr(VI) Reduction SynCom +description: A methane-oxidizing synthetic microbial community coupling Cr(VI) reduction to division of + labor and extracellular electron transfer. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Reveal division of labor in methane oxidation coupled to chromium reduction. + assembly_strategy: SynCom was constructed by controlling methane concentration and chromium load, enriching + Methylocystis with Hyphomicrobium and Thiobacillus partners. + perturbation_design: Methane concentration, chromium load, and methane oxidation inhibition. + measurement_endpoints: + - Cr(VI) removal load + - methane oxidation + - extracellular electron transfer + - multi-omics protein expression + evidence: + - &id001 + reference: PMID:41932525 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: In this study, a synthetic microbial community (SynCom) was constructed by controlling methane + concentration and chromium load. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Hypoxic methane-fed synthetic microbial community for chromium reduction. +taxonomy: +- taxon_term: + preferred_term: Methylocystis sp. + term: + id: NCBITaxon:133 + label: Methylocystis + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Hyphomicrobium sp. + term: + id: NCBITaxon:82 + label: Hyphomicrobium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Thiobacillus sp. + term: + id: NCBITaxon:919 + label: Thiobacillus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Methane-Driven Chromium Reduction + description: Methanotrophs and partner genera couple methane oxidation with Cr(VI) reduction through + extracellular electron transfer. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: SynCom was constructed by controlling methane concentration and chromium load, enriching Methylocystis + with Hyphomicrobium and Thiobacillus partners. + description: Methane concentration, chromium load, and methane oxidation inhibition. + evidence: + - *id001 diff --git a/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml b/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml new file mode 100644 index 00000000..75219d76 --- /dev/null +++ b/kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml @@ -0,0 +1,93 @@ +id: CommunityMech:000109 +name: Miscanthus REE Tailings Nitrogen SynCom10 +description: A ten-strain Miscanthus root-derived SynCom with nitrification and denitrification capabilities + for ammonia nitrogen removal in rare earth mine tailings. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Convert pollutant ammonia nitrogen into plant nutrients and enhance phytoremediation in REE + mine tailings. + assembly_strategy: Ten bacterial strains from Miscanthus floridulus roots representing Burkholderia, + Paraburkholderia, Curtobacterium, Leifsonia, and Sinomonas. + perturbation_design: Live versus dead SynCom inoculation, with and without Miscanthus plants in tailing + soil. + measurement_endpoints: + - ammonia nitrogen reduction + - shoot biomass + - root biomass + - nitrogen-cycle strain enrichment + evidence: + - &id001 + reference: PMID:39481489 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This SynCom, consisting of 10 bacterial strains, included species of the genera Burkholderia + (5) Paraburkholderia (1), Curtobacterium (1), Leifsonia (1) and Sinomonas (2). + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: contaminated soil + term: + id: ENVO:00002874 + label: contaminated soil + notes: Ionic rare earth mine tailing soil with high ammonia nitrogen. +taxonomy: +- taxon_term: + preferred_term: Burkholderia sp. + term: + id: NCBITaxon:32008 + label: Burkholderia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Paraburkholderia sp. + term: + id: NCBITaxon:1822464 + label: Paraburkholderia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Curtobacterium sp. + term: + id: NCBITaxon:2034 + label: Curtobacterium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Leifsonia sp. + term: + id: NCBITaxon:2025 + label: Leifsonia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Sinomonas sp. + term: + id: NCBITaxon:37927 + label: Sinomonas + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Nitrogen Transformation in REE Tailings + description: Root-derived bacteria couple nitrification, denitrification, and plant growth promotion + to remove ammonia nitrogen. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Ten bacterial strains from Miscanthus floridulus roots representing Burkholderia, Paraburkholderia, + Curtobacterium, Leifsonia, and Sinomonas. + description: Live versus dead SynCom inoculation, with and without Miscanthus plants in tailing soil. + evidence: + - *id001 diff --git a/kb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml b/kb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml new file mode 100644 index 00000000..1373fcf1 --- /dev/null +++ b/kb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml @@ -0,0 +1,56 @@ +id: CommunityMech:000117 +name: Multiomics Corn Straw Degradation SynCom +description: A core synthetic microbial community designed by multiomics linkage technology to degrade + corn straw lignocellulose. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: LIGNOCELLULOSE +engineering_design: + objective: Construct a functionally targeted SynCom for efficient lignocellulose degradation. + assembly_strategy: Species analysis and functional predictions across ecosystems were coupled to construct + a core synthetic microbial community. + perturbation_design: Solid-state fermentation optimization for inoculum level, nitrogen source ratio, + and fermentation time. + measurement_endpoints: + - cellulose degradation + - hemicellulose degradation + - lignin degradation + - proteomic enzyme profiles + evidence: + - &id001 + reference: PMID:37774801 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The synthetic microbial community was employed to degrade corn straw via solid-state fermentation. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Solid-state corn straw fermentation with an eight-strain lignocellulose-degrading SynCom. +taxonomy: +- taxon_term: + preferred_term: lignocellulose-degrading bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +ecological_interactions: +- name: Corn Straw Lignocellulose Degradation + description: A multi-strain community partitions enzymatic roles for cellulose, hemicellulose, and lignin + conversion. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Species analysis and functional predictions across ecosystems were coupled to construct a core + synthetic microbial community. + description: Solid-state fermentation optimization for inoculum level, nitrogen source ratio, and fermentation + time. + evidence: + - *id001 diff --git a/kb/communities/NCycle_Bioflocculation_Model_Consortium.yaml b/kb/communities/NCycle_Bioflocculation_Model_Consortium.yaml new file mode 100644 index 00000000..687837de --- /dev/null +++ b/kb/communities/NCycle_Bioflocculation_Model_Consortium.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000124 +name: N-Cycle Bioflocculation Model Consortium +description: A reduced-complexity N-cycle model consortium of nitrifiers and denitrifiers used to study + bioflocculation mechanisms in biological wastewater treatment. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOTECHNOLOGY +engineering_design: + objective: Build a reduced-complexity living model of activated sludge flocculation. + assembly_strategy: Nitrifying bacteria were entrapped to form microcolonies and then released with denitrifier + flocs to form macroclusters. + perturbation_design: Oxic/anoxic sequencing batch reactor cycles and alginate entrapment were used to + control aggregation. + measurement_endpoints: + - microcolony formation + - macrocluster formation + - bioflocculation + - FISH aggregation readouts + evidence: + - &id001 + reference: PMID:40536564 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: We show that it is feasible to exploit a model (N-cycle) consortium with reduced complexity + to fundamentally study bioflocculation. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: activated sludge floc model + term: + id: ENVO:00002046 + label: sludge + notes: Model consortium designed to emulate aggregation in biological wastewater treatment. +taxonomy: +- taxon_term: + preferred_term: N-cycle bacterial consortium members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Nitrifier-Denitrifier Aggregate Formation + description: Nitrifier microcolonies and denitrifier flocs formed larger aggregate structures under + reactor cycling. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: oxic/anoxic sequencing batch reactor cycling + value: Oxic/anoxic cycles and alginate entrapment were used to produce nitrifier microcolonies and mixed + aggregates. + description: Oxic/anoxic sequencing batch reactor cycles and alginate entrapment were used to control + aggregation. + evidence: + - *id001 diff --git a/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml b/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml new file mode 100644 index 00000000..acd45d80 --- /dev/null +++ b/kb/communities/Peanut_Seed_Bacterial_CS_SynCom.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000100 +name: Peanut Seed Bacterial CS SynCom +description: A combined peanut seed-borne bacterial synthetic community that suppresses Aspergillus flavus + and Fusarium oxysporum while promoting seedling growth. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Construct conserved, growth-promoting, and combined peanut seed bacterial SynComs for pathogen + resistance. + assembly_strategy: Synthetic communities were derived from 16S profiling, strain isolation, and plant + growth promotion indicators. + perturbation_design: Peanut seed and seedling pathogen challenges with Aspergillus flavus and Fusarium + oxysporum. + measurement_endpoints: + - root rot resistance + - aflatoxin suppression + - defense enzyme activity + - seedling growth + evidence: + - &id001 + reference: PMID:38520150 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Potentially conserved microbial synthetic communities (C), growth-promoting synthetic communities + (S), and combined synthetic communities (CS) of peanut seeds were constructed after 16S rRNA Illumina + sequencing, strain isolation, and measurement of plant growth promotion indicators. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Seed-borne peanut bacterial SynComs tested against seed and root fungal pathogens. +taxonomy: +- taxon_term: + preferred_term: peanut seed bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Seed-Borne Fungal Suppression + description: Seed-borne bacterial consortia suppress fungal invasion and stimulate host defense. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Synthetic communities were derived from 16S profiling, strain isolation, and plant growth promotion + indicators. + description: Peanut seed and seedling pathogen challenges with Aspergillus flavus and Fusarium oxysporum. + evidence: + - *id001 diff --git a/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml b/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml new file mode 100644 index 00000000..950e0f7f --- /dev/null +++ b/kb/communities/Pepper_Growth_Rhizosphere_SynCom.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000102 +name: Pepper Growth Rhizosphere SynCom +description: A pepper seedling SynCom treatment that enhances growth and root morphology by modulating + rhizosphere microbial communities. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Determine how SynCom inoculation at seedling stage enhances pepper growth and rhizosphere + microbiome structure. + assembly_strategy: Synthetic microbial community applied during pepper seedling establishment. + perturbation_design: SynCom inoculated versus uninoculated pepper seedlings. + measurement_endpoints: + - shoot height + - root vigor + - root length + - rhizosphere microbial diversity + - key taxa abundance + evidence: + - &id001 + reference: PMID:39858916 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper + growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Pepper seedling rhizosphere SynCom inoculation system. +taxonomy: +- taxon_term: + preferred_term: pepper rhizosphere SynCom bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Pepper Rhizosphere Growth Promotion + description: SynCom inoculation enriches growth-associated rhizosphere taxa and improves pepper root + traits. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Synthetic microbial community applied during pepper seedling establishment. + description: SynCom inoculated versus uninoculated pepper seedlings. + evidence: + - *id001 diff --git a/kb/communities/Pepper_Phytophthora_SynCom5.yaml b/kb/communities/Pepper_Phytophthora_SynCom5.yaml new file mode 100644 index 00000000..5ab31dcd --- /dev/null +++ b/kb/communities/Pepper_Phytophthora_SynCom5.yaml @@ -0,0 +1,84 @@ +id: CommunityMech:000103 +name: Pepper Phytophthora-Resistance SynCom5 +description: A five-isolate pepper rhizosphere SynCom that reduces Phytophthora capsici disease severity + and enhances pepper growth. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Evaluate a five-member bacterial SynCom for improving pepper resilience against Phytophthora + capsici. + assembly_strategy: Bacillus, Flavobacterium, Cytobacillus, Streptomyces, and Pseudomonas isolates from + healthy pepper rhizosphere. + perturbation_design: Pepper plants challenged with P. capsici after SynCom application. + measurement_endpoints: + - disease severity + - plant growth + - phosphate solubilization + - IAA production + - siderophore synthesis + evidence: + - &id001 + reference: PMID:40508300 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: We then applied this 5-isolate synthetic microbial community (SynCom) to Capsicum annuum + to evaluate its efficacy in improving pepper resilience against P. capsici. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Five-isolate pepper rhizosphere SynCom tested against Phytophthora capsici. +taxonomy: +- taxon_term: + preferred_term: Bacillus sp. + term: + id: NCBITaxon:1386 + label: Bacillus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Flavobacterium sp. + term: + id: NCBITaxon:237 + label: Flavobacterium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Streptomyces sp. + term: + id: NCBITaxon:1931 + label: Streptomyces sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Phytophthora Suppression + description: Rhizosphere isolates combine antagonism and plant growth-promoting traits to suppress pathogen + damage. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Bacillus, Flavobacterium, Cytobacillus, Streptomyces, and Pseudomonas isolates from healthy pepper + rhizosphere. + description: Pepper plants challenged with P. capsici after SynCom application. + evidence: + - *id001 diff --git a/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml b/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml new file mode 100644 index 00000000..bbb56154 --- /dev/null +++ b/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml @@ -0,0 +1,65 @@ +id: CommunityMech:000111 +name: Phylogenetically Diverse Denitrifying SynCom +description: Closely related and distantly related synthetic denitrifying communities used to test how + phylogenetic diversity affects denitrification and stability. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Determine whether phylogenetic diversity improves denitrification function and temporal stability. + assembly_strategy: Closely related communities used Shewanella strains; distantly related communities + used constituents from different genera. + perturbation_design: Experimental evolution for 200 generations. + measurement_endpoints: + - denitrification rate + - productivity + - temporal stability + - complementarity + evidence: + - &id001 + reference: PMID:37207729 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'we selected denitrifiers based on their phylogenetic distance to construct two groups of + synthetic denitrifying communities: one closely related (CR) group with all strains from the genus + Shewanella and the other distantly related (DR) group with all constituents from different genera.' + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Synthetic denitrifying communities experimentally evolved under laboratory conditions. +taxonomy: +- taxon_term: + preferred_term: Shewanella sp. + term: + id: NCBITaxon:22 + label: Shewanella + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Paracoccus denitrificans + term: + id: NCBITaxon:266 + label: Paracoccus denitrificans + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Phylogenetic Complementarity in Denitrification + description: Distantly related denitrifiers improve function and stability through complementarity and + asynchronous fluctuations. + interaction_type: NICHE_PARTITIONING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Closely related communities used Shewanella strains; distantly related communities used constituents + from different genera. + description: Experimental evolution for 200 generations. + evidence: + - *id001 diff --git a/kb/communities/Populus_Salt_Tolerant_SynComs.yaml b/kb/communities/Populus_Salt_Tolerant_SynComs.yaml new file mode 100644 index 00000000..d3607464 --- /dev/null +++ b/kb/communities/Populus_Salt_Tolerant_SynComs.yaml @@ -0,0 +1,57 @@ +id: CommunityMech:000088 +name: Populus Salt-Tolerant Rhizosphere SynComs +description: Function-driven Populus rhizosphere SynComs selected from high-salt soil to improve salt + resistance in hybrid poplar. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Tailor simplified salt-tolerant SynComs that confer salt stress resistance to Populus. + assembly_strategy: Isolate-select-construct workflow from 512 high-salt rhizosphere isolates, with nine + growth-promoting salt-tolerant strains selected. + perturbation_design: High-salinity plant stress assays comparing multiple SynCom formulations. + measurement_endpoints: + - salt-stress growth + - oxidative stress markers + - osmolyte adjustment + - ion balance + evidence: + - &id001 + reference: PMID:40904019 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: This study aimed to establish a framework (isolate-select-construct) for tailoring simplified + salt-tolerant synthetic microbial communities (SynComs) and explore how they confer salt stress + resistance to the plant. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Synthetic communities selected from high-salt Populus euphratica rhizosphere soil and tested + on hybrid poplar. +taxonomy: +- taxon_term: + preferred_term: Populus salt-tolerant rhizosphere bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Salt Stress Protection + description: Selected rhizosphere bacteria improve plant salt tolerance through oxidative stress, osmolyte, + and ion-balance mechanisms. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Isolate-select-construct workflow from 512 high-salt rhizosphere isolates, with nine growth-promoting + salt-tolerant strains selected. + description: High-salinity plant stress assays comparing multiple SynCom formulations. + evidence: + - *id001 diff --git a/kb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml b/kb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml new file mode 100644 index 00000000..c67e84a4 --- /dev/null +++ b/kb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml @@ -0,0 +1,64 @@ +id: CommunityMech:000090 +name: Rhodopseudomonas-E. coli Cross-Feeding Coculture +description: A reciprocal cross-feeding coculture pairing N2-fixing Rhodopseudomonas palustris with fermentative + Escherichia coli. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOTECHNOLOGY +engineering_design: + objective: Test whether nutrient uptake adaptation can drive emergence of reciprocal cross-feeding. + assembly_strategy: Two-member coculture based on nitrogen transfer from R. palustris and carbon-rich + fermentation product transfer from E. coli. + perturbation_design: Wild-type and engineered cross-feeding contexts were compared during coculture + evolution. + measurement_endpoints: + - ammonium uptake + - fermentation product exchange + - recipient adaptation + - coculture growth + evidence: + - &id001 + reference: PMID:32788711 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Previously we engineered a cross-feeding coculture between N2-fixing Rhodopseudomonas palustris + and fermentative Escherichia coli. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Engineered and evolved two-member cross-feeding coculture. +taxonomy: +- taxon_term: + preferred_term: Rhodopseudomonas palustris + term: + id: NCBITaxon:1076 + label: Rhodopseudomonas palustris + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +- taxon_term: + preferred_term: Escherichia coli + term: + id: NCBITaxon:562 + label: Escherichia coli + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Reciprocal Carbon-Nitrogen Cross-Feeding + description: R. palustris supplies ammonium while E. coli supplies fermentation products. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Two-member coculture based on nitrogen transfer from R. palustris and carbon-rich fermentation + product transfer from E. coli. + description: Wild-type and engineered cross-feeding contexts were compared during coculture evolution. + evidence: + - *id001 diff --git a/kb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml b/kb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml new file mode 100644 index 00000000..ac042bcd --- /dev/null +++ b/kb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml @@ -0,0 +1,54 @@ +id: CommunityMech:000107 +name: Rice Acid Soil Bioinoculant SynCom +description: A customized rhizosphere-competent bacterial SynCom used as a bioinoculant to improve rice + production in acid soils. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Overcome acid soil and aluminum toxicity constraints in rice using selected rhizosphere-competent + bacteria. + assembly_strategy: Carefully selected rhizosphere-competent bacterial strains composed the rice bioinoculant + SynCom. + perturbation_design: Acid soil and aluminum toxicity stress. + measurement_endpoints: + - rice growth + - rice yield + - soil acidity resistance + - aluminum toxicity resistance + evidence: + - &id001 + reference: PMID:38324131 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: A customised synthetic microbial community (SynCom) composed of carefully selected rhizosphere-competent + bacterial strains improved rice growth, yield and resistance to soil acidity and Al toxicity. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: contaminated soil + term: + id: ENVO:00002874 + label: contaminated soil + notes: Acid soil with aluminum toxicity constraints for rice production. +taxonomy: +- taxon_term: + preferred_term: rice rhizosphere-competent bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Rice Acid-Soil Stress Mitigation + description: Rhizosphere competent bacteria improve rice growth and yield under acid soil stress. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Carefully selected rhizosphere-competent bacterial strains composed the rice bioinoculant SynCom. + description: Acid soil and aluminum toxicity stress. + evidence: + - *id001 diff --git a/kb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml b/kb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml new file mode 100644 index 00000000..f6122dec --- /dev/null +++ b/kb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml @@ -0,0 +1,84 @@ +id: CommunityMech:000108 +name: Rice Phosphorus Uptake Intercropping SynCom4 +description: A four-strain rice rhizosphere SynCom from intercropping systems that enhances biomass and + phosphorus uptake. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Harness intercropping-associated bacteria to improve rice phosphorus acquisition. + assembly_strategy: Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, and + Acidovorax sp. were assembled into a bacterial SynCom. + perturbation_design: Pot experiments testing rice growth and phosphorus uptake after SynCom inoculation. + measurement_endpoints: + - biomass + - phosphorus uptake + - soil available phosphorus + - root morphology + - phosphate transporter expression + evidence: + - &id001 + reference: PMID:39684532 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: A bacterial synthetic community (SynCom) composed of four bacterial strains (Variovorax paradoxus, + Novosphingobium subterraneum, Hydrogenophaga pseudoflava, Acidovorax sp.) significantly enhanced + the biomass and P uptake of potted rice plants. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Rice rhizosphere SynCom isolated from rice-soybean intercropping systems. +taxonomy: +- taxon_term: + preferred_term: Variovorax paradoxus + term: + id: NCBITaxon:34073 + label: Variovorax paradoxus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Novosphingobium subterraneum + term: + id: NCBITaxon:48935 + label: Novosphingobium subterraneum + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Hydrogenophaga pseudoflava + term: + id: NCBITaxon:47421 + label: Hydrogenophaga pseudoflava + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Acidovorax sp. + term: + id: NCBITaxon:12916 + label: Acidovorax + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Phosphorus Acquisition Promotion + description: SynCom members increase soil available phosphorus and support root-to-shoot phosphorus + transport. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, and Acidovorax + sp. were assembled into a bacterial SynCom. + description: Pot experiments testing rice growth and phosphorus uptake after SynCom inoculation. + evidence: + - *id001 diff --git a/kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml b/kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml new file mode 100644 index 00000000..d6c7698a --- /dev/null +++ b/kb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml @@ -0,0 +1,153 @@ +id: CommunityMech:000082 +name: Streptococcus mutans - Candida albicans ECC Biofilm Model +description: >- + A defined cross-kingdom dual-species plaque biofilm model capturing the + synergistic virulence of Streptococcus mutans and Candida albicans in early + childhood caries. Coinfection produces an EPS-rich biofilm with higher + biomass, larger microcolonies, and more severe carious lesions than either + species alone. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: >- + Test whether a dual-species bacterium-fungus consortium amplifies plaque + biofilm virulence and caries severity beyond single-species infections. + assembly_strategy: >- + Bottom-up assembly of Streptococcus mutans and Candida albicans in + cospecies plaque biofilms, followed by validation in a rodent caries model. + perturbation_design: >- + Cospecies biofilms were compared with single-species controls in vitro and + in vivo to measure EPS production, biofilm architecture, virulence gene + expression, and caries severity. + measurement_endpoints: + - Biofilm biomass + - EPS accumulation + - Virulence gene expression + - Three-dimensional biofilm imaging + - Rodent caries scoring + evidence: + - reference: PMID:24566629 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + We showed that the ability of these organisms together to form biofilms + is enhanced in vitro and in vivo. + explanation: Supports the defined dual-species design and its enhanced biofilm phenotype. +environment_term: + preferred_term: cariogenic plaque biofilm on tooth surface + term: + id: ENVO:01001034 + label: environment determined by a biofilm on an animal surface + notes: >- + Cross-kingdom plaque biofilm model relevant to early childhood caries and + validated on rodent tooth surfaces in vivo. +taxonomy: +- taxon_term: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + evidence: + - reference: PMID:24566629 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + Streptococcus mutans is often cited as the main bacterial pathogen in + dental caries, particularly in early-childhood caries (ECC). + explanation: Establishes Streptococcus mutans as the bacterial member of the model. +- taxon_term: + preferred_term: Candida albicans + term: + id: NCBITaxon:5476 + label: Candida albicans + evidence: + - reference: PMID:24566629 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + Candida albicans cells are frequently detected along with heavy + infection by S. mutans in plaque biofilms from ECC-affected children. + explanation: Establishes Candida albicans as the fungal member of the model. +ecological_interactions: +- name: Cross-Kingdom Biofilm Enhancement + description: >- + Coinoculation of Streptococcus mutans and Candida albicans enhances biofilm + formation relative to either species alone in both in vitro and in vivo + settings. + interaction_type: MUTUALISM + source_taxon: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + target_taxon: + preferred_term: Candida albicans + term: + id: NCBITaxon:5476 + label: Candida albicans + evidence: + - reference: PMID:24566629 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + We showed that the ability of these organisms together to form biofilms + is enhanced in vitro and in vivo. + explanation: Supports a mutually reinforcing cross-kingdom biofilm interaction. +- name: Candida-Driven EPS Amplification of Streptococcus mutans + description: >- + Candida albicans promotes an EPS-rich matrix and higher viable Streptococcus + mutans abundance within cospecies plaque biofilms. + interaction_type: COLONIZATION_FACILITATION + source_taxon: + preferred_term: Candida albicans + term: + id: NCBITaxon:5476 + label: Candida albicans + target_taxon: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + evidence: + - reference: PMID:24566629 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + The presence of C. albicans augments the production of + exopolysaccharides (EPS), such that cospecies biofilms accrue more + biomass and harbor more viable S. mutans cells than single-species + biofilms. + explanation: Supports Candida-mediated enhancement of S. mutans colonization and matrix formation. +- name: Synergistic Caries Virulence + description: >- + Coinfection with Streptococcus mutans and Candida albicans increases plaque + infection burden and produces more aggressive carious lesions than either + species alone. + interaction_type: COLONIZATION_FACILITATION + source_taxon: + preferred_term: Candida albicans + term: + id: NCBITaxon:5476 + label: Candida albicans + target_taxon: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + evidence: + - reference: PMID:24566629 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + Coinfected animals displayed higher levels of infection and microbial + carriage within plaque biofilms than animals infected with either species + alone. + explanation: Documents increased pathogenic load during dual-species coinfection. + - reference: PMID:24566629 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + Furthermore, coinfection synergistically enhanced biofilm virulence, + leading to aggressive onset of the disease with rampant carious lesions. + explanation: Documents amplified caries severity caused by the dual-species consortium. diff --git a/kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml b/kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml new file mode 100644 index 00000000..106cf605 --- /dev/null +++ b/kb/communities/SMutans_SSputigena_ECC_Pathobiont.yaml @@ -0,0 +1,127 @@ +id: CommunityMech:000083 +name: Streptococcus mutans - Selenomonas sputigena ECC Pathobiont Model +description: >- + A defined dual-species oral biofilm model derived from early childhood caries + discovery-validation work. Selenomonas sputigena becomes trapped within + Streptococcus mutans exoglucans, builds a honeycomb-like multicellular + superstructure, enhances acidogenesis, and increases enamel lesion severity + in vivo. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: >- + Identify disease-relevant inter-species interactions in early childhood + caries and validate whether Selenomonas sputigena acts as a pathobiont with + Streptococcus mutans. + assembly_strategy: >- + Discovery-validation pipeline starting from supragingival biofilm + metagenomics and metatranscriptomics, followed by dual-species imaging, + virulence assays, and rodent coinfection experiments. + perturbation_design: >- + Selenomonas sputigena was tested individually and with Streptococcus + mutans to compare spatial arrangement, acidogenesis, tooth-surface + colonization, and in vivo cariogenicity. + measurement_endpoints: + - Metagenomics + - Metatranscriptomics + - Multiscale imaging + - Virulence assays + - Rodent caries scoring + evidence: + - reference: PMID:37217495 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + Here, we integrate multi-omics of supragingival biofilm (dental plaque) + from 416 preschool-age children (208 males and 208 females) in a + discovery-validation pipeline to identify disease-relevant inter-species + interactions. + explanation: Supports the study design used to derive and validate this pathobiont model. +environment_term: + preferred_term: supragingival cariogenic plaque biofilm + term: + id: ENVO:01001034 + label: environment determined by a biofilm on an animal surface + notes: >- + Model is grounded in supragingival plaque from preschool children with + early childhood caries and validated on tooth surfaces in vivo. +taxonomy: +- taxon_term: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + evidence: + - reference: PMID:37217495 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + Streptococcus mutans has been implicated as the primary pathogen in + childhood caries (tooth decay). + explanation: Establishes Streptococcus mutans as the reference pathogen in the model. +- taxon_term: + preferred_term: Selenomonas sputigena + term: + id: NCBITaxon:69823 + label: Selenomonas sputigena + evidence: + - reference: PMID:37217495 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + We show that S. sputigena, a flagellated anaerobe with previously unknown + role in supragingival biofilm, becomes trapped in streptococcal + exoglucans + explanation: Establishes Selenomonas sputigena as the pathobiont evaluated in the model. +ecological_interactions: +- name: Streptococcal Exoglucan Entrapment of Selenomonas sputigena + description: >- + Streptococcus mutans exoglucans trap Selenomonas sputigena, suppress its + motility, and create a structured mixed-species biofilm. + interaction_type: COLONIZATION_FACILITATION + source_taxon: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + target_taxon: + preferred_term: Selenomonas sputigena + term: + id: NCBITaxon:69823 + label: Selenomonas sputigena + evidence: + - reference: PMID:37217495 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + We show that S. sputigena, a flagellated anaerobe with previously unknown + role in supragingival biofilm, becomes trapped in streptococcal + exoglucans, loses motility but actively proliferates to build a + honeycomb-like multicellular-superstructure encapsulating S. mutans, + enhancing acidogenesis. + explanation: Documents matrix-mediated trapping and structured coassembly with S. mutans. +- name: Pathobiont-Enhanced Cariogenicity + description: >- + Selenomonas sputigena is non-cariogenic alone but markedly worsens enamel + lesion formation when coinfected with Streptococcus mutans. + interaction_type: COLONIZATION_FACILITATION + source_taxon: + preferred_term: Selenomonas sputigena + term: + id: NCBITaxon:69823 + label: Selenomonas sputigena + target_taxon: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + evidence: + - reference: PMID:37217495 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + While incapable of causing caries on its own, when co-infected with S. + mutans, S. sputigena causes extensive tooth enamel lesions and + exacerbates disease severity in vivo. + explanation: Supports S. sputigena as a pathobiont that heightens S. mutans virulence. diff --git a/kb/communities/SMutans_VParvula_ASC_Biofilm.yaml b/kb/communities/SMutans_VParvula_ASC_Biofilm.yaml new file mode 100644 index 00000000..41804cef --- /dev/null +++ b/kb/communities/SMutans_VParvula_ASC_Biofilm.yaml @@ -0,0 +1,129 @@ +id: CommunityMech:000084 +name: Streptococcus mutans - Veillonella parvula Adult Severe Caries Model +description: >- + A defined dual-species oral biofilm model for adult severe caries pairing + Streptococcus mutans with the ASC-associated pathobiont Veillonella parvula. + The coculture increases mature biofilm formation, acid resistance, oxidative + stress tolerance, and rodent caries severity relative to Streptococcus + mutans alone. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: >- + Identify adult severe caries-associated taxa and test whether Veillonella + parvula enhances Streptococcus mutans biofilm virulence. + assembly_strategy: >- + Metagenomic identification of adult severe caries-associated taxa followed + by defined dual-species coculture and rodent caries experiments with + Streptococcus mutans and Veillonella parvula. + perturbation_design: >- + Dual-species biofilms were evaluated for acidification, aciduricity, + oxidative stress tolerance, gtf expression, EPS synthesis, and in vivo + cariogenicity relative to single-species controls. + measurement_endpoints: + - Metagenomic profiling + - Acidification assays + - Aciduricity assays + - Oxidative stress tolerance assays + - EPS imaging + - Rodent caries scoring + evidence: + - reference: PMID:39345197 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + Samples of dental plaque were collected for metagenomic analysis. The + acidification, aciduricity, oxidative stress tolerance, and gtf + (glucosyltransferase) gene expression of S. mutans cocultured with V. + parvula + explanation: Supports the design of the dual-species adult severe caries model. +environment_term: + preferred_term: adult severe caries plaque biofilm + term: + id: ENVO:01001034 + label: environment determined by a biofilm on an animal surface + notes: >- + Defined plaque biofilm model motivated by metagenomic analysis of adult + severe caries and validated with rodent infection experiments. +taxonomy: +- taxon_term: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + evidence: + - reference: PMID:39345197 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + This study is focused on the composition of dental plaque microbiome + profiles in order to identify disease-relevant species and to investigate + into their interactions with the S. mutans. + explanation: Establishes Streptococcus mutans as the reference pathogen in the model. +- taxon_term: + preferred_term: Veillonella parvula + term: + id: NCBITaxon:29466 + label: Veillonella parvula + abundance_level: DOMINANT + evidence: + - reference: PMID:39345197 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + The most significantly abundant taxon found associated with ASC was V. + parvula. + explanation: Establishes Veillonella parvula as the adult severe caries-associated pathobiont. +ecological_interactions: +- name: Veillonella parvula Promotion of Streptococcus mutans Biofilm Virulence + description: >- + Veillonella parvula promotes mature Streptococcus mutans biofilm formation + and increases stress tolerance and virulence traits in the dual-species + consortium. + interaction_type: COLONIZATION_FACILITATION + source_taxon: + preferred_term: Veillonella parvula + term: + id: NCBITaxon:29466 + label: Veillonella parvula + target_taxon: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + evidence: + - reference: PMID:39345197 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + In vitro experiments found that V. parvula can effectively promote S. + mutans mature biofilm formation with enhanced acid resistance, hydrogen + peroxide detoxicity, and biofilm virulence. + explanation: Supports Veillonella-driven enhancement of S. mutans virulence traits. +- name: Pathobiont-Driven Adult Severe Caries Exacerbation + description: >- + Veillonella parvula is not independently cariogenic in the model but + significantly worsens disease progression when coinfected with + Streptococcus mutans. + interaction_type: COLONIZATION_FACILITATION + source_taxon: + preferred_term: Veillonella parvula + term: + id: NCBITaxon:29466 + label: Veillonella parvula + target_taxon: + preferred_term: Streptococcus mutans + term: + id: NCBITaxon:1309 + label: Streptococcus mutans + evidence: + - reference: PMID:39345197 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: >- + Rodent model experiments revealed that V. parvula was incapable of + causing disease on its own, but it significantly heightened the biofilm + virulence of S. mutans when being co-infected and augmented the + progression, quantity, and severity of dental caries. + explanation: Supports Veillonella parvula as a synergistic pathobiont in adult severe caries. diff --git a/kb/communities/Shewanella_Denitrifying_Richness_SynComs.yaml b/kb/communities/Shewanella_Denitrifying_Richness_SynComs.yaml new file mode 100644 index 00000000..43896009 --- /dev/null +++ b/kb/communities/Shewanella_Denitrifying_Richness_SynComs.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000112 +name: Shewanella Denitrifying Richness SynComs +description: A panel of synthetic denitrifying communities assembled from 12 Shewanella denitrifiers with + richness spanning one to twelve species. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Measure biodiversity-ecosystem functioning relationships during microbial experimental evolution. + assembly_strategy: Random selection from a 12-member Shewanella denitrifier candidate pool to create + richness-gradient communities. + perturbation_design: Approximately 180 days of experimental evolution with 60 transfers. + measurement_endpoints: + - productivity + - denitrification rate + - community richness + - evolutionary change + evidence: + - &id001 + reference: PMID:37154752 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) + with a richness gradient spanning 1 to 12 species + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Synthetic denitrifying communities with Shewanella richness gradient. +taxonomy: +- taxon_term: + preferred_term: Shewanella denitrifiers + term: + id: NCBITaxon:22 + label: Shewanella + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Richness-Dependent Denitrification + description: Shewanella richness gradients produce dynamic biodiversity-function relationships during + evolution. + interaction_type: NICHE_PARTITIONING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Random selection from a 12-member Shewanella denitrifier candidate pool to create richness-gradient + communities. + description: Approximately 180 days of experimental evolution with 60 transfers. + evidence: + - *id001 diff --git a/kb/communities/SkinCom_Synthetic_Skin_Community.yaml b/kb/communities/SkinCom_Synthetic_Skin_Community.yaml new file mode 100644 index 00000000..0425f548 --- /dev/null +++ b/kb/communities/SkinCom_Synthetic_Skin_Community.yaml @@ -0,0 +1,55 @@ +id: CommunityMech:000123 +name: SkinCom Synthetic Skin Community +description: A standardized synthetic skin microbial community for reproducible in vitro and in vivo studies + of skin-associated microbe-metabolite interactions. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Create a reproducible microbial component for experimental human skin microbiome models. + assembly_strategy: Aerobic and anaerobic skin-associated bacteria were assembled into the SkinCom standardized + community. + perturbation_design: SkinCom was tested with common cosmetic chemicals in vitro and on dorsal skin of + mice in vivo. + measurement_endpoints: + - community reproducibility + - DNA and RNA recovery + - chemical response agreement + - microbe-metabolite interactions + evidence: + - &id001 + reference: PMID:39111313 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: SkinCom represents a valuable, standardized tool for investigating microbe-metabolite interactions + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: skin-associated microbial habitat + term: + id: UBERON:0002097 + label: skin of body + notes: Synthetic community applied to skin and skin-like experimental systems. +taxonomy: +- taxon_term: + preferred_term: skin bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Skin Microbe-Metabolite Response + description: The standardized SkinCom enables reproducible assays of microbial responses to skin-relevant + chemicals. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: standardized skin model conditions + value: SkinCom was evaluated in vitro and after application to dorsal skin of mice. + description: SkinCom was tested with common cosmetic chemicals in vitro and on dorsal skin of mice in + vivo. + evidence: + - *id001 diff --git a/kb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml b/kb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml new file mode 100644 index 00000000..898b441a --- /dev/null +++ b/kb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml @@ -0,0 +1,67 @@ +id: CommunityMech:000127 +name: Soybean Chlorophyll-Selected Biofertilizer SynCom +description: A plant-guided soybean rhizosphere SynCom selected through iterative chlorophyll-based microbiome + engineering to improve nodulation and biomass in soil. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Develop a multi-member soybean biofertilizer SynCom using host-mediated microbiome engineering. + assembly_strategy: A starting consortium of Bradyrhizobium spp. and non-rhizobial soil isolates was + recurrently selected using leaf chlorophyll content. + perturbation_design: Eight consecutive gnotobiotic selection rounds were followed by evaluation in non-sterile + soil. + measurement_endpoints: + - leaf chlorophyll content + - rhizosphere community composition + - nodule number + - plant biomass + - nitrogen transformation potential + evidence: + - &id001 + reference: PMID:42007760 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: a synthetic microbial community (SynCom) was developed through a host-mediated microbiome + engineering approach guided by leaf chlorophyll content as a rapid, non-destructive plant trait. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: soybean rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Soybean-associated rhizosphere community selected under gnotobiotic and non-sterile soil conditions. +taxonomy: +- taxon_term: + preferred_term: soybean rhizosphere bacterial SynCom members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Bradyrhizobium + term: + id: NCBITaxon:374 + label: Bradyrhizobium + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +ecological_interactions: +- name: Plant-Guided Beneficial Rhizosphere Assembly + description: Recurrent host-mediated selection favored nodulating Bradyrhizobium and associated beneficial + rhizosphere taxa. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: chlorophyll-guided recurrent selection + value: Rhizosphere communities from superior soybean performers were pooled and propagated across selection + rounds. + description: Eight consecutive gnotobiotic selection rounds were followed by evaluation in non-sterile + soil. + evidence: + - *id001 diff --git a/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml b/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml new file mode 100644 index 00000000..3aac63f6 --- /dev/null +++ b/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml @@ -0,0 +1,59 @@ +id: CommunityMech:000125 +name: SynComBac10 Chicken Intestinal SynCom +description: A 10-member synthetic chicken intestinal community that promotes gut homeostasis and anti-Salmonella + immunity through segmented filamentous bacteria establishment. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Manipulate chicken gut microbiota development and anti-infection immunity with a designed + microbial consortium. + assembly_strategy: Ten intestinal bacterial members were selected to recapitulate adult chicken intestinal + phylogenetic diversity and functional capability. + perturbation_design: Early-life exposure and Salmonella infection challenge were used to test gut maturation + and immune resistance. + measurement_endpoints: + - growth performance + - epithelial barrier maturation + - segmented filamentous bacteria colonization + - Th17 immune response + - Salmonella resistance + evidence: + - &id001 + reference: PMID:40266232 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: we constructed a 10-member synthetic microbial community (SynComBac10) that recapitulated + the phylogenetic diversity and functional capability of adult chicken intestinal microbiota. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: chicken intestine + term: + id: UBERON:0000160 + label: intestine + notes: Designed chicken intestinal microbiota used in early-life exposure experiments. +taxonomy: +- taxon_term: + preferred_term: chicken intestinal SynComBac10 members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: SynCom-Stimulated SFB Cross-Feeding + description: SynComBac10-derived metabolites likely facilitate early establishment of segmented filamentous + bacteria. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: early-life gut SynCom exposure + value: Chickens were exposed early in life to SynComBac10 and evaluated for gut maturation and Salmonella + resistance. + description: Early-life exposure and Salmonella infection challenge were used to test gut maturation + and immune resistance. + evidence: + - *id001 diff --git a/kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml b/kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml new file mode 100644 index 00000000..2acdee95 --- /dev/null +++ b/kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml @@ -0,0 +1,74 @@ +id: CommunityMech:000128 +name: Synthetic Periphyton Freshwater Biofilm +description: A 26-member phototrophic synthetic periphyton biofilm used as a reproducible freshwater model + system for species dynamics and stressor response. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: PHYTOPLANKTON +engineering_design: + objective: Create a controlled synthetic periphyton model for manipulating freshwater phototrophic biofilm + species dynamics. + assembly_strategy: Twenty-six phototrophic species including diatoms, green algae, and cyanobacteria + were inoculated in successional sequence onto glass slides. + perturbation_design: Temperature increase and herbicide stressors were applied singly and in combination. + measurement_endpoints: + - species-level abundance dynamics + - community reproducibility + - biofilm function + - 3D spatial structure + - stressor response + evidence: + - &id001 + reference: PMID:35869094 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we rationally developed a workflow to construct a synthetic community by co-culturing 26 + phototrophic species (i.e., diatoms, green algae, and cyanobacteria) + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: freshwater periphyton biofilm + term: + id: ENVO:01001242 + label: freshwater environment + notes: Synthetic periphytic biofilm grown on glass slides under controlled conditions. +taxonomy: +- taxon_term: + preferred_term: diatoms + term: + id: NCBITaxon:2836 + label: Bacillariophyta + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +- taxon_term: + preferred_term: green algae + term: + id: NCBITaxon:3041 + label: Chlorophyta + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +- taxon_term: + preferred_term: cyanobacteria + term: + id: NCBITaxon:1117 + label: Cyanobacteria + functional_role: + - PRIMARY_PRODUCER + evidence: + - *id001 +ecological_interactions: +- name: Successional Periphyton Biofilm Assembly + description: Phototrophic species assemble into a diverse, stable, reproducible biofilm with trackable + species dynamics. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: successional inoculation on glass slides + value: Phototrophic species were inoculated sequentially to construct a synthetic periphytic biofilm. + description: Temperature increase and herbicide stressors were applied singly and in combination. + evidence: + - *id001 diff --git a/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml b/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml new file mode 100644 index 00000000..2cae7461 --- /dev/null +++ b/kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml @@ -0,0 +1,84 @@ +id: CommunityMech:000098 +name: Teosinte-Derived Maize Biofertilizer SynCom7 +description: A seven-strain teosinte-derived bacterial SynCom tested as a maize biofertilizer under conventional + and precision fertilization strategies. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Modulate maize microbiome composition, growth, yield, and soil functionality using teosinte-associated + bacteria. + assembly_strategy: Seven bacterial strains from teosinte-associated microbes were formulated as a SynCom. + perturbation_design: Conventional fertilization, drone-assisted precision delivery, and SynCom biofertilization + were compared. + measurement_endpoints: + - maize plant performance + - soil bacterial community shifts + - soil fungal community shifts + - beneficial taxa abundance + evidence: + - &id001 + reference: PMID:40270813 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'This SynCom consisted of seven bacterial strains: Serratia nematodiphila EDR2, Klebsiella + variicola EChLG19, Bacillus thuringiensis EML22, Pantoea agglomerans EMH25, Bacillus thuringiensis + EBG39, Serratia marcescens EPLG52, and Bacillus tropicus EPP72.' + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Seven teosinte-associated bacteria applied as maize biofertilizer. +taxonomy: +- taxon_term: + preferred_term: Serratia sp. + term: + id: NCBITaxon:613 + label: Serratia + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Klebsiella variicola + term: + id: NCBITaxon:244366 + label: Klebsiella variicola + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Bacillus thuringiensis + term: + id: NCBITaxon:1428 + label: Bacillus thuringiensis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pantoea agglomerans + term: + id: NCBITaxon:549 + label: Pantoea agglomerans + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Teosinte-Maize Biofertilization + description: Teosinte-associated SynCom members reshape maize-associated microbial communities and enrich + beneficial taxa. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Seven bacterial strains from teosinte-associated microbes were formulated as a SynCom. + description: Conventional fertilization, drone-assisted precision delivery, and SynCom biofertilization + were compared. + evidence: + - *id001 diff --git a/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml b/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml new file mode 100644 index 00000000..39edde90 --- /dev/null +++ b/kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml @@ -0,0 +1,64 @@ +id: CommunityMech:000104 +name: Tobacco Chemotactic Biocontrol SynCom +description: A chemotactic three-member SynCom in bioorganic fertilizer for suppressing Ralstonia solanacearum + in tobacco fields. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Construct a chemotactic SynCom with compatibility, antagonism, and chemotaxis traits for + bacterial wilt control. + assembly_strategy: Two Pseudomonas strains and one Bacillus strain selected from healthy tobacco rhizosphere + isolates. + perturbation_design: Bioorganic fertilizer formulation plus growth-promoting metabolites including vitamin + C, propionic acid, and esculetin. + measurement_endpoints: + - Ralstonia suppression + - tobacco yield + - chemotaxis marker presence + - rhizosphere community enrichment + evidence: + - &id001 + reference: PMID:40670700 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: we constructed a chemotactic SynCom comprising two Pseudomonas strains and one Bacillus strain. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Chemotactic tobacco rhizosphere SynCom delivered in bioorganic fertilizer. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Bacillus sp. + term: + id: NCBITaxon:1386 + label: Bacillus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Chemotactic Bacterial Wilt Suppression + description: Chemotactic SynCom members colonize the rhizosphere and suppress Ralstonia invasion. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Two Pseudomonas strains and one Bacillus strain selected from healthy tobacco rhizosphere isolates. + description: Bioorganic fertilizer formulation plus growth-promoting metabolites including vitamin C, + propionic acid, and esculetin. + evidence: + - *id001 diff --git a/kb/communities/Tomato_Oxylipin_SynCom3.yaml b/kb/communities/Tomato_Oxylipin_SynCom3.yaml new file mode 100644 index 00000000..42aacac4 --- /dev/null +++ b/kb/communities/Tomato_Oxylipin_SynCom3.yaml @@ -0,0 +1,74 @@ +id: CommunityMech:000105 +name: Tomato Oxylipin-Protective SynCom3 +description: A three-species simplified tomato rhizosphere SynCom that steers oxylipin pathways and protects + against Botrytis cinerea. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Use pathogen-induced and stably colonizing rhizosphere bacteria to intensify plant defense + oxylipin pathways. + assembly_strategy: A 38-species community was simplified to Asticcacaulis, Arachidicoccus, and Phenylobacterium + representatives. + perturbation_design: Botrytis cinerea foliar infection and tomato oxylipin pathway perturbation. + measurement_endpoints: + - gray mold protection + - biofilm formation + - defense response triggering + - divinyl ether production + evidence: + - &id001 + reference: PMID:37549573 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Through the analysis of the rhizosphere bacterial community, we established a synthetic community + harboring 8 phytopathogen-inducible and 30 stably-colonizing bacteria species. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Tomato rhizosphere SynCom simplified from phytopathogen-inducible and stably colonizing bacteria. +taxonomy: +- taxon_term: + preferred_term: Asticcacaulis sp. + term: + id: NCBITaxon:76890 + label: Asticcacaulis + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Arachidicoccus sp. + term: + id: NCBITaxon:1499392 + label: Arachidicoccus + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Phenylobacterium sp. + term: + id: NCBITaxon:28448 + label: Phenylobacterium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Oxylipin-Mediated Disease Resistance + description: Inducible and stable colonizers synergize to trigger host defense and biofilm-mediated + protection. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: A 38-species community was simplified to Asticcacaulis, Arachidicoccus, and Phenylobacterium + representatives. + description: Botrytis cinerea foliar infection and tomato oxylipin pathway perturbation. + evidence: + - *id001 diff --git a/kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml b/kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml new file mode 100644 index 00000000..7be22c58 --- /dev/null +++ b/kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml @@ -0,0 +1,76 @@ +id: CommunityMech:000110 +name: Tribromophenol Anaerobic Bioremediation SynCom +description: A synthetic anaerobic community with Clostridium, Dehalobacter, and Desulfatiglans functions + for 2,4,6-tribromophenol mineralization. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOREMEDIATION +engineering_design: + objective: Mineralize 2,4,6-tribromophenol to carbon dioxide through coordinated reductive debromination, + fermentation, and phenol degradation. + assembly_strategy: Dehalobacter phylotype FTH1, Clostridium strain Ma13, and Desulfatiglans parachlorophenolica + strain DS were combined functionally. + perturbation_design: Optimization of glucose, sulfate, and inoculum density under anaerobic conditions. + measurement_endpoints: + - tribromophenol mineralization + - phenol degradation + - debromination + - carbon dioxide production + evidence: + - &id001 + reference: PMID:25461007 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Anaerobic mineralization of 2,4,6-tribromophenol (2,4,6-TBP) was achieved by a synthetic + anaerobe community comprising a highly enriched culture of Dehalobacter sp. phylotype FTH1 acting + as a reductive debrominator; Clostridium sp. strain Ma13 acting as a hydrogen supplier via glucose + fermentation; and a novel 4-chlorophenol-degrading anaerobe, Desulfatiglans parachlorophenolica + strain DS. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Anaerobic laboratory consortium for halogenated aromatic mineralization. +taxonomy: +- taxon_term: + preferred_term: Dehalobacter sp. + term: + id: NCBITaxon:55552 + label: Dehalobacter + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Clostridium sp. + term: + id: NCBITaxon:1485 + label: Clostridium + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Desulfatiglans parachlorophenolica + term: + id: NCBITaxon:1121382 + label: Desulfatiglans parachlorophenolica + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Anaerobic Halophenol Mineralization + description: Debromination, hydrogen supply, and phenol degradation are partitioned among members. + interaction_type: SYNTROPHY + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Dehalobacter phylotype FTH1, Clostridium strain Ma13, and Desulfatiglans parachlorophenolica + strain DS were combined functionally. + description: Optimization of glucose, sulfate, and inoculum density under anaerobic conditions. + evidence: + - *id001 diff --git a/kb/communities/Urine_Nitrification_SynCom.yaml b/kb/communities/Urine_Nitrification_SynCom.yaml new file mode 100644 index 00000000..53c17bc2 --- /dev/null +++ b/kb/communities/Urine_Nitrification_SynCom.yaml @@ -0,0 +1,91 @@ +id: CommunityMech:000115 +name: Urine Nitrification Synthetic Microbial Community +description: A five-member synthetic microbial community containing nitrifiers and ureolytic heterotrophs + for urine nitrification. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: BIOTECHNOLOGY +engineering_design: + objective: Convert urine nitrogen to nitrate fertilizer while managing salinity and organic compounds. + assembly_strategy: Nitrosomonas europaea, Nitrobacter winogradskyi, Pseudomonas fluorescens, Acidovorax + delafieldii, and Delftia acidovorans were compiled. + perturbation_design: Salt adaptation and urine feeding in nitrification reactors. + measurement_endpoints: + - ammonium removal + - nitrate production + - salt adaptation + - organic removal + evidence: + - &id001 + reference: PMID:31623889 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: In this study, a synthetic microbial community containing an AOB (Nitrosomonas europaea), + NOB (Nitrobacter winogradskyi), and three ureolytic heterotrophs (Pseudomonas fluorescens, Acidovorax + delafieldii, and Delftia acidovorans) was compiled and evaluated for these challenges. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Synthetic and real urine nitrification reactors. +taxonomy: +- taxon_term: + preferred_term: Nitrosomonas europaea + term: + id: NCBITaxon:915 + label: Nitrosomonas europaea + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Nitrobacter winogradskyi + term: + id: NCBITaxon:913 + label: Nitrobacter winogradskyi + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Pseudomonas fluorescens + term: + id: NCBITaxon:294 + label: Pseudomonas fluorescens + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Acidovorax delafieldii + term: + id: NCBITaxon:80867 + label: Acidovorax delafieldii + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: Delftia acidovorans + term: + id: NCBITaxon:80866 + label: Delftia acidovorans + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Nitrifier-Heterotroph Urine Conversion + description: Ureolytic heterotrophs and nitrifiers cooperate to convert urine nitrogen to nitrate. + interaction_type: CROSS_FEEDING + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Nitrosomonas europaea, Nitrobacter winogradskyi, Pseudomonas fluorescens, Acidovorax delafieldii, + and Delftia acidovorans were compiled. + description: Salt adaptation and urine feeding in nitrification reactors. + evidence: + - *id001 diff --git a/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml b/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml new file mode 100644 index 00000000..1645d319 --- /dev/null +++ b/kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml @@ -0,0 +1,66 @@ +id: CommunityMech:000096 +name: Watermelon Rhizosphere Fusarium-Protective SynCom8 +description: A simplified eight-member watermelon rhizosphere SynCom derived from an initial 16-member + grafted-watermelon core community. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: RHIZOSPHERE +engineering_design: + objective: Use synergistic rhizosphere bacteria to protect watermelon against Fusarium oxysporum and + promote growth. + assembly_strategy: Initial 16 core bacterial strains from grafted watermelon rhizosphere were refined + to eight synergistic bacteria centered on Pseudomonas. + perturbation_design: Ungrafted watermelon grown in non-sterile soil under soil-borne disease pressure. + measurement_endpoints: + - plant growth + - disease resistance + - Pseudomonas abundance + - biofilm-forming pathways + evidence: + - &id001 + reference: PMID:38840214 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained + from the rhizosphere of grafted watermelon plants. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: Grafted watermelon rhizosphere-derived SynCom protecting ungrafted watermelon in non-sterile + soil. +taxonomy: +- taxon_term: + preferred_term: Pseudomonas sp. + term: + id: NCBITaxon:306 + label: Pseudomonas sp. + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +- taxon_term: + preferred_term: watermelon rhizosphere bacteria + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Synergistic Watermelon Disease Suppression + description: Pseudomonas and partner bacteria act synergistically to improve plant growth and disease + resistance. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Initial 16 core bacterial strains from grafted watermelon rhizosphere were refined to eight synergistic + bacteria centered on Pseudomonas. + description: Ungrafted watermelon grown in non-sterile soil under soil-borne disease pressure. + evidence: + - *id001 diff --git a/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml b/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml new file mode 100644 index 00000000..a1e881a8 --- /dev/null +++ b/kb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml @@ -0,0 +1,86 @@ +id: CommunityMech:000116 +name: Wheat Straw Biogas Pretreatment SynCom +description: A four-member bacterial-fungal synthetic microbial community that produces enzymes for wheat + straw pretreatment and enhanced biogas production. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: LIGNOCELLULOSE +engineering_design: + objective: Improve lignocellulose degradation and biogas production from wheat straw. + assembly_strategy: Core microorganisms with lignocellulose-degrading abilities were screened from straw + and forest environments and combined. + perturbation_design: Synthetic microbial community enzyme pretreatment compared with commercial enzyme + pretreatments. + measurement_endpoints: + - cellulose degradation + - hemicellulose degradation + - lignin degradation + - cumulative biogas production + evidence: + - &id001 + reference: PMID:38748977 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 'Herein, a metagenomic approach was used to screen core microorganisms (Bacillus subtilis, + Acinetobacter johnsonii, Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading + abilities among samples from three environments: pile retting wheat straw (WS), WS returned to soil, + and forest soil.' + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: laboratory bioreactor + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: Synthetic microbial community for enzyme production and wheat straw pretreatment before anaerobic + digestion. +taxonomy: +- taxon_term: + preferred_term: Bacillus subtilis + term: + id: NCBITaxon:1423 + label: Bacillus subtilis + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Acinetobacter johnsonii + term: + id: NCBITaxon:40214 + label: Acinetobacter johnsonii + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Trichoderma viride + term: + id: NCBITaxon:5544 + label: Trichoderma viride + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +- taxon_term: + preferred_term: Aspergillus niger + term: + id: NCBITaxon:5061 + label: Aspergillus niger + functional_role: + - PRIMARY_DEGRADER + evidence: + - *id001 +ecological_interactions: +- name: Lignocellulose Enzyme Pretreatment + description: Bacterial and fungal enzyme producers jointly degrade wheat straw polymers before anaerobic + digestion. + interaction_type: MUTUALISM + evidence: + - *id001 +environmental_factors: +- name: defined synthetic community design + value: Core microorganisms with lignocellulose-degrading abilities were screened from straw and forest + environments and combined. + description: Synthetic microbial community enzyme pretreatment compared with commercial enzyme pretreatments. + evidence: + - *id001 diff --git a/kb/communities/hCom2_Complex_Gut_Microbiome.yaml b/kb/communities/hCom2_Complex_Gut_Microbiome.yaml new file mode 100644 index 00000000..3d7ffd07 --- /dev/null +++ b/kb/communities/hCom2_Complex_Gut_Microbiome.yaml @@ -0,0 +1,58 @@ +id: CommunityMech:000121 +name: hCom2 Complex Gut Microbiome +description: A complex defined human gut microbiome assembled from hCom1 and iteratively augmented after + fecal challenge to improve stability and colonization resistance in gnotobiotic mice. +ecological_state: ENGINEERED +community_origin: SYNTHETIC +community_category: OTHER +engineering_design: + objective: Construct a defined but complex gut microbiome that models human gut community functions + in vivo. + assembly_strategy: A 104-species hCom1 community was challenged with fecal microbiota in germ-free mice + and augmented with engrafting species to yield hCom2. + perturbation_design: Fecal challenge and pathogenic Escherichia coli challenge were used to test stability + and colonization resistance. + measurement_endpoints: + - engraftment + - community stability + - colonization resistance + - host phenotypes + evidence: + - &id001 + reference: PMID:36070752 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: We identified new species that engrafted following fecal challenge and added them to hCom1, + yielding hCom2. + explanation: Supports the defined synthetic community design and represented community context. +environment_term: + preferred_term: human gut + term: + id: UBERON:0001007 + label: digestive system + notes: Defined human gut microbiome used in gnotobiotic mouse experiments. +taxonomy: +- taxon_term: + preferred_term: defined human gut bacterial members + term: + id: NCBITaxon:2 + label: Bacteria + functional_role: + - CROSS_FEEDER + evidence: + - *id001 +ecological_interactions: +- name: Gut Niche Filling and Colonization Resistance + description: Iterative niche filling improved stability to fecal challenge and resistance to pathogenic + Escherichia coli. + interaction_type: COLONIZATION_FACILITATION + evidence: + - *id001 +environmental_factors: +- name: gnotobiotic fecal challenge + value: Germ-free mice colonized with hCom1 were challenged with a human fecal sample to identify additional + engrafting species. + description: Fecal challenge and pathogenic Escherichia coli challenge were used to test stability and + colonization resistance. + evidence: + - *id001 diff --git a/references_cache/PMID_36154140.md b/references_cache/PMID_36154140.md new file mode 100644 index 00000000..45edffba --- /dev/null +++ b/references_cache/PMID_36154140.md @@ -0,0 +1,96 @@ +--- +reference_id: PMID:36154140 +title: Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes. +authors: +- McClure R +- Farris Y +- Danczak R +- Nelson W +- Song HS +- Kessell A +- Lee JY +- Couvillion S +- Henry C +- Jansson JK +- Hofmockel KS +journal: mSystems +year: '2022' +doi: 10.1128/msystems.00372-22 +keywords: +- Chitin/metabolism +- Soil/chemistry +- Microbiota/genetics +- Carbon +- Nitrogen/metabolism +content_type: abstract_only +--- + +# Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes. +**Authors:** McClure R, Farris Y, Danczak R, Nelson W, Song HS, Kessell A, Lee JY, Couvillion S, Henry C, Jansson JK, Hofmockel KS +**Journal:** mSystems (2022) +**DOI:** [10.1128/msystems.00372-22](https://doi.org/10.1128/msystems.00372-22) + +## Content + +1. mSystems. 2022 Oct 26;7(5):e0037222. doi: 10.1128/msystems.00372-22. Epub 2022 + Sep 26. + +Interaction Networks Are Driven by Community-Responsive Phenotypes in a +Chitin-Degrading Consortium of Soil Microbes. + +McClure R(1), Farris Y(1), Danczak R(1), Nelson W(1), Song HS(2)(3), Kessell +A(2), Lee JY(1), Couvillion S(1), Henry C(4), Jansson JK(1), Hofmockel KS(1)(5). + +Author information: +(1)Biological Sciences Division, Pacific Northwest National +Laboratorygrid.451303.0, Richland, Washington, USA. +(2)Department of Biological Systems Engineering, University of Nebraska-Lincoln, +Lincoln, Nebraska, USA. +(3)Department of Food Science and Technology, Nebraska Food for Health Center, +University of Nebraska-Lincoln, Lincoln, Nebraska, USA. +(4)Data Science and Learning Division, Argonne National Laboratory, Lemont, +Illinois, USA. +(5)Department of Agronomy, Iowa State University, Ames, Iowa, USA. + +Soil microorganisms provide key ecological functions that often rely on +metabolic interactions between individual populations of the soil microbiome. To +better understand these interactions and community processes, we used chitin, a +major carbon and nitrogen source in soil, as a test substrate to investigate +microbial interactions during its decomposition. Chitin was applied to a model +soil consortium that we developed, "model soil consortium-2" (MSC-2), consisting +of eight members of diverse phyla and including both chitin degraders and +nondegraders. A multiomics approach revealed how MSC-2 community-level processes +during chitin decomposition differ from monocultures of the constituent species. +Emergent properties of both species and the community were found, including +changes in the chitin degradation potential of Streptomyces species and +organization of all species into distinct roles in the chitin degradation +process. The members of MSC-2 were further evaluated via metatranscriptomics and +community metabolomics. Intriguingly, the most abundant members of MSC-2 were +not those that were able to metabolize chitin itself, but rather those that were +able to take full advantage of interspecies interactions to grow on chitin +decomposition products. Using a model soil consortium greatly increased our +knowledge of how carbon is decomposed and metabolized in a community setting, +showing that niche size, rather than species metabolic capacity, can drive +success and that certain species become active carbon degraders only in the +context of their surrounding community. These conclusions fill important +knowledge gaps that are key to our understanding of community interactions that +support carbon and nitrogen cycling in soil. IMPORTANCE The soil microbiome +performs many functions that are key to ecology, agriculture, and nutrient +cycling. However, because of the complexity of this ecosystem we do not know the +molecular details of the interactions between microbial species that lead to +these important functions. Here, we use a representative but simplified model +community of bacteria to understand the details of these interactions. We show +that certain species act as primary degraders of carbon sources and that the +most successful species are likely those that can take the most advantage of +breakdown products, not necessarily the primary degraders. We also show that a +species phenotype, including whether it is a primary degrader or not, is driven +in large part by the membership of the community it resides in. These +conclusions are critical to a better understanding of the soil microbial +interaction network and how these interactions drive central soil microbiome +functions. + +DOI: 10.1128/msystems.00372-22 +PMCID: PMC9599572 +PMID: 36154140 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/PMID_40904019.md b/references_cache/PMID_40904019.md new file mode 100644 index 00000000..e0b531c2 --- /dev/null +++ b/references_cache/PMID_40904019.md @@ -0,0 +1,72 @@ +--- +reference_id: PMID:40904019 +title: Rhizosphere Microbes From Populus euphratica Conferred Salt Stress Resistance to Populus alba × Populus glandulosa. +authors: +- Li L +- Cheng K +- Du Y +- Zhang Y +- Zhou Y +- Jin Y +- He X +journal: Plant Cell Environ +year: '2025' +doi: 10.1111/pce.70160 +keywords: +- "Populus/microbiology, physiology" +- Rhizosphere +- Salt Stress +- Soil Microbiology +- Salt Tolerance +- Plant Roots/microbiology +- Microbiota/physiology +- Salt-Tolerant Plants +content_type: abstract_only +--- + +# Rhizosphere Microbes From Populus euphratica Conferred Salt Stress Resistance to Populus alba × Populus glandulosa. +**Authors:** Li L, Cheng K, Du Y, Zhang Y, Zhou Y, Jin Y, He X +**Journal:** Plant Cell Environ (2025) +**DOI:** [10.1111/pce.70160](https://doi.org/10.1111/pce.70160) + +## Content + +1. Plant Cell Environ. 2025 Dec;48(12):8743-8755. doi: 10.1111/pce.70160. Epub +2025 Sep 3. + +Rhizosphere Microbes From Populus euphratica Conferred Salt Stress Resistance to +Populus alba × Populus glandulosa. + +Li L(1)(2), Cheng K(2), Du Y(2), Zhang Y(2), Zhou Y(2), Jin Y(2), He X(1)(2). + +Author information: +(1)State Key Laboratory of Efficient Production of Forest Resources, Beijing +Forestry University, Beijing, China. +(2)College of Biological Sciences and Technology, Beijing Forestry University, +Beijing, China. + +The rhizosphere microbiomes of halophytes are crucial for plant adaptation to +high-salinity soil conditions, but how to harness rhizosphere microbes to confer +salt stress resistance to plants remains obscure. This study aimed to establish +a framework (isolate-select-construct) for tailoring simplified salt-tolerant +synthetic microbial communities (SynComs) and explore how they confer salt +stress resistance to the plant. First, a total of 512 strains were isolated from +the high-salt rhizosphere soil of Populus euphratica through high-throughput +cultivation. Among these, nine strains were further selected for their +salt-tolerant and growth-promoting abilities, with three isolates identified as +key microbes, including hub microbes, keystone taxa and biomarkers. Guided by a +function-driven strategy, we constructed five distinct SynComs, with SynCom5, +SynCom7 and SynCom9 showing the most significant improvement in the growth of +hybrid Poplar 84K (Populus alba × Populus glandulosa). Mechanistic +investigations revealed that these SynComs can increase resistance to salt +stress by directly reducing oxidative stress, adjusting osmolytes and balancing +ions. Additionally, these SynComs were observed to recruit specific +root-associated bacterial consortia that enhance the adaptability of poplar to +salt stress. Overall, this study lays the groundwork for designing SynComs that +promote plant growth and offers insights into harnessing specific microbial +communities to boost plants' salt resistance. + +© 2025 John Wiley & Sons Ltd. + +DOI: 10.1111/pce.70160 +PMID: 40904019 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_21966490.txt b/references_cache/pmid_21966490.txt new file mode 100644 index 00000000..813fb94f --- /dev/null +++ b/references_cache/pmid_21966490.txt @@ -0,0 +1,50 @@ +1. PLoS One. 2011;6(9):e25299. doi: 10.1371/journal.pone.0025299. Epub 2011 Sep +23. + +pH landscapes in a novel five-species model of early dental biofilm. + +Schlafer S(1), Raarup MK, Meyer RL, Sutherland DS, Dige I, Nyengaard JR, Nyvad +B. + +Author information: +(1)iNANO The Interdisciplinary Nanoscience Center, Faculty of Science, Aarhus +University, Aarhus, Denmark. sebastian.schlafer@hotmail.de + +BACKGROUND: Despite continued preventive efforts, dental caries remains the most +common disease of man. Organic acids produced by microorganisms in dental plaque +play a crucial role for the development of carious lesions. During early stages +of the pathogenetic process, repeated pH drops induce changes in microbial +composition and favour the establishment of an increasingly acidogenic and +aciduric microflora. The complex structure of dental biofilms, allowing for a +multitude of different ecological environments in close proximity, remains +largely unexplored. In this study, we designed a laboratory biofilm model that +mimics the bacterial community present during early acidogenic stages of the +caries process. We then performed a time-resolved microscopic analysis of the +extracellular pH landscape at the interface between bacterial biofilm and +underlying substrate. +METHODOLOGY/PRINCIPAL FINDINGS: Strains of Streptococcus oralis, Streptococcus +sanguinis, Streptococcus mitis, Streptococcus downei and Actinomyces naeslundii +were employed in the model. Biofilms were grown in flow channels that allowed +for direct microscopic analysis of the biofilms in situ. The architecture and +composition of the biofilms were analysed using fluorescence in situ +hybridization and confocal laser scanning microscopy. Both biofilm structure and +composition were highly reproducible and showed similarity to in-vivo-grown +dental plaque. We employed the pH-sensitive ratiometric probe C-SNARF-4 to +perform real-time microscopic analyses of the biofilm pH in response to salivary +solutions containing glucose. Anaerobic glycolysis in the model biofilms created +a mildly acidic environment. Decrease in pH in different areas of the biofilms +varied, and distinct extracellular pH-microenvironments were conserved over +several hours. +CONCLUSIONS/SIGNIFICANCE: The designed biofilm model represents a promising tool +to determine the effect of potential therapeutic agents on biofilm growth, +composition and extracellular pH. Ratiometric pH analysis using C-SNARF-4 gives +detailed insight into the pH landscape of living biofilms and contributes to our +general understanding of metabolic processes in in-vivo-grown bacterial +biofilms. + +DOI: 10.1371/journal.pone.0025299 +PMCID: PMC3179500 +PMID: 21966490 [Indexed for MEDLINE] + +Conflict of interest statement: Competing Interests: The authors have declared +that no competing interests exist. \ No newline at end of file diff --git a/references_cache/pmid_23446436.txt b/references_cache/pmid_23446436.txt new file mode 100644 index 00000000..c8498e9c --- /dev/null +++ b/references_cache/pmid_23446436.txt @@ -0,0 +1,36 @@ +1. Caries Res. 2013;47(4):318-24. doi: 10.1159/000347050. Epub 2013 Feb 27. + +A defined-multispecies microbial model for studying enamel caries development. + +Arthur RA(1), Waeiss RA, Hara AT, Lippert F, Eckert GJ, Zero DT. + +Author information: +(1)Oral Health Research Institute, Department of Preventive and Community +Dentistry, Indiana University School of Dentistry, Indianapolis, Ind., USA. + +The aims of this study were to describe and validate an in vitro multispecies +microbial biofilm model for caries development by evaluating the effects of +varying medium concentration of sucrose (0.5 and 1.0%) and fluoride (0.4, 0.8 +and 1.0 ppm F) in study 1, and calcium (1.0 and 2.0 mM Ca) in study 2. +Defined-multispecies biofilms, formed by Lactobacillus casei, Streptococcus +mutans, S. salivarius and S. sanguinis, were grown on the surface of +salivary-pellicle-coated enamel slabs, with known baseline surface hardness; +growth medium was changed daily. Counts of viable cells on biofilms and the +percentage of surface microhardness change (%SMC), lesion depth (LD) and +integrated mineral loss (IML) on enamel slabs were assessed after 4 days of +biofilm formation under the tested conditions. Counts of viable cells on +biofilms were significantly affected by sucrose, fluoride and calcium +concentrations (p < 0.05). There was a decrease in %SMC in response to increased +fluoride and calcium concentrations (p < 0.001). Lower IML (p < 0.001) and LD (p +< 0.05) were found in the presence of 0.8 and 1.0 ppm F. A negative correlation +was found between the response variables (%SMC, LD and IML) and fluoride and +calcium concentrations. The results suggest that the microbial caries model +developed was able to show distinct levels of caries inhibition in response to +fluoride and calcium concentrations, corroborating clinical observations. An +effect of sucrose concentration on caries development was found only in the +presence of the lowest fluoride concentration. + +Copyright © 2013 S. Karger AG, Basel. + +DOI: 10.1159/000347050 +PMID: 23446436 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_24566629.txt b/references_cache/pmid_24566629.txt new file mode 100644 index 00000000..cd788c8b --- /dev/null +++ b/references_cache/pmid_24566629.txt @@ -0,0 +1,42 @@ +1. Infect Immun. 2014 May;82(5):1968-81. doi: 10.1128/IAI.00087-14. Epub 2014 Feb + 24. + +Symbiotic relationship between Streptococcus mutans and Candida albicans +synergizes virulence of plaque biofilms in vivo. + +Falsetta ML(1), Klein MI, Colonne PM, Scott-Anne K, Gregoire S, Pai CH, +Gonzalez-Begne M, Watson G, Krysan DJ, Bowen WH, Koo H. + +Author information: +(1)Center for Oral Biology, University of Rochester Medical Center, Rochester, +New York, USA. + +Streptococcus mutans is often cited as the main bacterial pathogen in dental +caries, particularly in early-childhood caries (ECC). S. mutans may not act +alone; Candida albicans cells are frequently detected along with heavy infection +by S. mutans in plaque biofilms from ECC-affected children. It remains to be +elucidated whether this association is involved in the enhancement of biofilm +virulence. We showed that the ability of these organisms together to form +biofilms is enhanced in vitro and in vivo. The presence of C. albicans augments +the production of exopolysaccharides (EPS), such that cospecies biofilms accrue +more biomass and harbor more viable S. mutans cells than single-species +biofilms. The resulting 3-dimensional biofilm architecture displays sizeable S. +mutans microcolonies surrounded by fungal cells, which are enmeshed in a dense +EPS-rich matrix. Using a rodent model, we explored the implications of this +cross-kingdom interaction for the pathogenesis of dental caries. Coinfected +animals displayed higher levels of infection and microbial carriage within +plaque biofilms than animals infected with either species alone. Furthermore, +coinfection synergistically enhanced biofilm virulence, leading to aggressive +onset of the disease with rampant carious lesions. Our in vitro data also +revealed that glucosyltransferase-derived EPS is a key mediator of cospecies +biofilm development and that coexistence with C. albicans induces the expression +of virulence genes in S. mutans (e.g., gtfB, fabM). We also found that +Candida-derived β1,3-glucans contribute to the EPS matrix structure, while +fungal mannan and β-glucan provide sites for GtfB binding and activity. +Altogether, we demonstrate a novel mutualistic bacterium-fungus relationship +that occurs at a clinically relevant site to amplify the severity of a +ubiquitous infectious disease. + +DOI: 10.1128/IAI.00087-14 +PMCID: PMC3993459 +PMID: 24566629 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_24743269.txt b/references_cache/pmid_24743269.txt new file mode 100644 index 00000000..4f6505b2 --- /dev/null +++ b/references_cache/pmid_24743269.txt @@ -0,0 +1,42 @@ +1. PLoS Genet. 2014 Apr 17;10(4):e1004283. doi: 10.1371/journal.pgen.1004283. +eCollection 2014 Apr. + +A synthetic community approach reveals plant genotypes affecting the +phyllosphere microbiota. + +Bodenhausen N(1), Bortfeld-Miller M(1), Ackermann M(2), Vorholt JA(1). + +Author information: +(1)Institute of Microbiology, ETH Zurich, Zurich, Switzerland. +(2)Department of Environmental Sciences, ETH Zurich, Zurich, Switzerland; +Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland. + +The identity of plant host genetic factors controlling the composition of the +plant microbiota and the extent to which plant genes affect associated microbial +populations is currently unknown. Here, we use a candidate gene approach to +investigate host effects on the phyllosphere community composition and +abundance. To reduce the environmental factors that might mask genetic factors, +the model plant Arabidopsis thaliana was used in a gnotobiotic system and +inoculated with a reduced complexity synthetic bacterial community composed of +seven strains representing the most abundant phyla in the phyllosphere. From a +panel of 55 plant mutants with alterations in the surface structure, cell wall, +defense signaling, secondary metabolism, and pathogen recognition, a small +number of single host mutations displayed an altered microbiota composition +and/or abundance. Host alleles that resulted in the strongest perturbation of +the microbiota relative to the wild-type were lacs2 and pec1. These mutants +affect cuticle formation and led to changes in community composition and an +increased bacterial abundance relative to the wild-type plants, suggesting that +different bacteria can benefit from a modified cuticle to different extents. +Moreover, we identified ein2, which is involved in ethylene signaling, as a host +factor modulating the community's composition. Finally, we found that different +Arabidopsis accessions exhibited different communities, indicating that plant +host genetic factors shape the associated microbiota, thus harboring significant +potential for the identification of novel plant factors affecting the microbiota +of the communities. + +DOI: 10.1371/journal.pgen.1004283 +PMCID: PMC3990490 +PMID: 24743269 [Indexed for MEDLINE] + +Conflict of interest statement: The authors have declared that no competing +interests exist. \ No newline at end of file diff --git a/references_cache/pmid_25461007.txt b/references_cache/pmid_25461007.txt new file mode 100644 index 00000000..6ed4e1c9 --- /dev/null +++ b/references_cache/pmid_25461007.txt @@ -0,0 +1,53 @@ +1. Bioresour Technol. 2015 Jan;176:225-32. doi: 10.1016/j.biortech.2014.10.097. +Epub 2014 Oct 25. + +Anaerobic mineralization of 2,4,6-tribromophenol to CO2 by a synthetic microbial +community comprising Clostridium, Dehalobacter, and Desulfatiglans. + +Li Z(1), Yoshida N(2), Wang A(3), Nan J(4), Liang B(5), Zhang C(6), Zhang D(7), +Suzuki D(6), Zhou X(8), Xiao Z(7), Katayama A(9). + +Author information: +(1)State Key Laboratory of Urban Water Resources and Environment, Harbin +Institute of Technology (SKLUWRE, HIT), Harbin 150090, China; EcoTopia Science +Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan. +(2)Center for Fostering Young and Innovative Researchers, Nagoya Institute of +Technology, Syowa, Nagoya 466-8555, Japan. +(3)State Key Laboratory of Urban Water Resources and Environment, Harbin +Institute of Technology (SKLUWRE, HIT), Harbin 150090, China; Key Laboratory of +Environmental Biotechnology, Research Center for Eco-Environmental Sciences, +Chinese Academy of Sciences, Beijing 100085, China. +(4)State Key Laboratory of Urban Water Resources and Environment, Harbin +Institute of Technology (SKLUWRE, HIT), Harbin 150090, China. +(5)Key Laboratory of Environmental Biotechnology, Research Center for +Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. +(6)EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, +Japan. +(7)Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, +Japan. +(8)Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8601, +Japan. +(9)EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, +Japan; Graduate School of Engineering, Nagoya University, Chikusa, Nagoya +464-8603, Japan; Graduate School of Environmental Studies, Nagoya University, +Nagoya 464-8601, Japan. Electronic address: a-katayama@esi.nagoya-u.ac.jp. + +Anaerobic mineralization of 2,4,6-tribromophenol (2,4,6-TBP) was achieved by a +synthetic anaerobe community comprising a highly enriched culture of +Dehalobacter sp. phylotype FTH1 acting as a reductive debrominator; Clostridium +sp. strain Ma13 acting as a hydrogen supplier via glucose fermentation; and a +novel 4-chlorophenol-degrading anaerobe, Desulfatiglans parachlorophenolica +strain DS. 2,4,6-TBP was debrominated to phenol by the combined action of Ma13 +and FTH1, then mineralized into CO2 by sequential introduction of DS, confirmed +using [ring-(14)C(U)] phenol. The optimum concentrations of glucose, SO4(2-), +and inoculum densities were 0.5 or 2.5mM, 1.0 or 2.5mM, and the densities +equivalent to 10(4)copiesmL(-1) of the 16S rRNA genes, respectively. This +resulted in the complete mineralization of 23μM 2,4,6-TBP within 35days +(0.58μmolL(-1)d(-1)). Thus, using a synthetic microbial community of isolates or +highly enriched cultures would be an efficient, optimizable, low-cost strategy +for anaerobic bioremediation of halogenated aromatics. + +Copyright © 2014 Elsevier Ltd. All rights reserved. + +DOI: 10.1016/j.biortech.2014.10.097 +PMID: 25461007 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_29152587.txt b/references_cache/pmid_29152587.txt new file mode 100644 index 00000000..e304613d --- /dev/null +++ b/references_cache/pmid_29152587.txt @@ -0,0 +1,48 @@ +1. mSystems. 2017 Nov 14;2(6):e00129-17. doi: 10.1128/mSystems.00129-17. +eCollection 2017 Nov-Dec. + +A Synthetic Community System for Probing Microbial Interactions Driven by +Exometabolites. + +Chodkowski JL(1), Shade A(1)(2). + +Author information: +(1)Department of Microbiology and Molecular Genetics, Michigan State University, +East Lansing, Michigan, USA. +(2)Department of Plant, Soil and Microbial Sciences, Program in Ecology, +Evolutionary Biology, and Behavior, The DOE Great Lakes Bioenergy Center, and +The Plant Resilience Institute, Michigan State University, East Lansing, +Michigan, USA. + +Though most microorganisms live within a community, we have modest knowledge +about microbial interactions and their implications for community properties and +ecosystem functions. To advance understanding of microbial interactions, we +describe a straightforward synthetic community system that can be used to +interrogate exometabolite interactions among microorganisms. The filter plate +system (also known as the Transwell system) physically separates microbial +populations, but allows for chemical interactions via a shared medium reservoir. +Exometabolites, including small molecules, extracellular enzymes, and +antibiotics, are assayed from the reservoir using sensitive mass spectrometry. +Community member outcomes, such as growth, productivity, and gene regulation, +can be determined using flow cytometry, biomass measurements, and transcript +analyses, respectively. The synthetic community design allows for determination +of the consequences of microbiome diversity for emergent community properties +and for functional changes over time or after perturbation. Because it is +versatile, scalable, and accessible, this synthetic community system has the +potential to practically advance knowledge of microbial interactions that occur +within both natural and artificial communities. IMPORTANCE Understanding +microbial interactions is a fundamental objective in microbiology and ecology. +The synthetic community system described here can set into motion a range of +research to investigate how the diversity of a microbiome and interactions among +its members impact its function, where function can be measured as +exometabolites. The system allows for community exometabolite profiling to be +coupled with genome mining, transcript analysis, and measurements of member +productivity and population size. It can also facilitate discovery of natural +products that are only produced within microbial consortia. Thus, this synthetic +community system has utility to address fundamental questions about a diversity +of possible microbial interactions that occur in both natural and engineered +ecosystems. + +DOI: 10.1128/mSystems.00129-17 +PMCID: PMC5686522 +PMID: 29152587 \ No newline at end of file diff --git a/references_cache/pmid_29930200.txt b/references_cache/pmid_29930200.txt new file mode 100644 index 00000000..b89fd473 --- /dev/null +++ b/references_cache/pmid_29930200.txt @@ -0,0 +1,50 @@ +1. Mol Syst Biol. 2018 Jun 21;14(6):e8157. doi: 10.15252/msb.20178157. + +Deciphering microbial interactions in synthetic human gut microbiome +communities. + +Venturelli OS(1), Carr AC(2), Fisher G(2), Hsu RH(3), Lau R(2), Bowen BP(2), +Hromada S(4), Northen T(2), Arkin AP(2)(3)(5)(6). + +Author information: +(1)Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA +venturelli@wisc.edu. +(2)Environmental Genomics and Systems Biology, Lawrence Berkeley National +Laboratory, Berkeley, CA, USA. +(3)California Institute for Quantitative Biosciences, University of California +Berkeley, Berkeley, CA, USA. +(4)Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, +USA. +(5)Department of Bioengineering, University of California Berkeley, Berkeley, +CA, USA. +(6)Energy Biosciences Institute, University of California Berkeley, Berkeley, +CA, USA. + +Comment in + Mol Syst Biol. 2018 Jun 21;14(6):e8425. doi: 10.15252/msb.20188425. + Nat Methods. 2018 Aug;15(8):572. doi: 10.1038/s41592-018-0094-z. + +The ecological forces that govern the assembly and stability of the human gut +microbiota remain unresolved. We developed a generalizable model-guided +framework to predict higher-dimensional consortia from time-resolved +measurements of lower-order assemblages. This method was employed to decipher +microbial interactions in a diverse human gut microbiome synthetic community. We +show that pairwise interactions are major drivers of multi-species community +dynamics, as opposed to higher-order interactions. The inferred ecological +network exhibits a high proportion of negative and frequent positive +interactions. Ecological drivers and responsive recipient species were +discovered in the network. Our model demonstrated that a prevalent positive and +negative interaction topology enables robust coexistence by implementing a +negative feedback loop that balances disparities in monospecies fitness levels. +We show that negative interactions could generate history-dependent responses of +initial species proportions that frequently do not originate from bistability. +Measurements of extracellular metabolites illuminated the metabolic capabilities +of monospecies and potential molecular basis of microbial interactions. In sum, +these methods defined the ecological roles of major human-associated intestinal +species and illuminated design principles of microbial communities. + +© 2018 The Authors. Published under the terms of the CC BY 4.0 license. + +DOI: 10.15252/msb.20178157 +PMCID: PMC6011841 +PMID: 29930200 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_31152139.txt b/references_cache/pmid_31152139.txt new file mode 100644 index 00000000..ccd05040 --- /dev/null +++ b/references_cache/pmid_31152139.txt @@ -0,0 +1,46 @@ +1. Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12558-12565. doi: +10.1073/pnas.1820691116. Epub 2019 May 31. + +Plant-derived coumarins shape the composition of an Arabidopsis synthetic root +microbiome. + +Voges MJEEE(1)(2), Bai Y(3), Schulze-Lefert P(3)(4), Sattely ES(5)(6). + +Author information: +(1)Department of Chemical Engineering, Stanford University, Stanford, CA 94305. +(2)Department of Bioengineering, Stanford University, Stanford, CA 94305. +(3)Department of Plant Microbe Interactions, Max Planck Institute for Plant +Breeding Research, 50829 Cologne, Germany. +(4)Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant +Breeding Research, 50829 Cologne, Germany. +(5)Department of Chemical Engineering, Stanford University, Stanford, CA 94305; +sattely@stanford.edu. +(6)Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305. + +The factors that contribute to the composition of the root microbiome and, in +turn, affect plant fitness are not well understood. Recent work has highlighted +a major contribution of the soil inoculum in determining the composition of the +root microbiome. However, plants are known to conditionally exude a diverse +array of unique secondary metabolites, that vary among species and environmental +conditions and can interact with the surrounding biota. Here, we explore the +role of specialized metabolites in dictating which bacteria reside in the +rhizosphere. We employed a reduced synthetic community (SynCom) of Arabidopsis +thaliana root-isolated bacteria to detect community shifts that occur in the +absence of the secreted small-molecule phytoalexins, flavonoids, and coumarins. +We find that lack of coumarin biosynthesis in f6'h1 mutant plant lines causes a +shift in the root microbial community specifically under iron deficiency. We +demonstrate a potential role for iron-mobilizing coumarins in sculpting the A. +thaliana root bacterial community by inhibiting the proliferation of a +relatively abundant Pseudomonas species via a redox-mediated mechanism. This +work establishes a systematic approach enabling elucidation of specific +mechanisms by which plant-derived molecules mediate microbial community +composition. Our findings expand on the function of conditionally exuded +specialized metabolites and suggest avenues to effectively engineer the +rhizosphere with the aim of improving crop growth in iron-limited alkaline +soils, which make up a third of the world's arable soils. + +DOI: 10.1073/pnas.1820691116 +PMCID: PMC6589675 +PMID: 31152139 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_31623889.txt b/references_cache/pmid_31623889.txt new file mode 100644 index 00000000..a74a0282 --- /dev/null +++ b/references_cache/pmid_31623889.txt @@ -0,0 +1,56 @@ +1. Syst Appl Microbiol. 2019 Nov;42(6):126021. doi: 10.1016/j.syapm.2019.126021. +Epub 2019 Sep 23. + +Urine nitrification with a synthetic microbial community. + +Christiaens MER(1), De Paepe J(2), Ilgrande C(1), De Vrieze J(1), Barys J(2), +Teirlinck P(1), Meerbergen K(3), Lievens B(4), Boon N(1), Clauwaert P(1), +Vlaeminck SE(5). + +Author information: +(1)Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure +Links 653, 9000 Gent, Belgium. +(2)Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure +Links 653, 9000 Gent, Belgium; Department of Chemical, Biological and +Environmental Engineering, School of Engineering, Universitat Autònoma de +Barcelona, Bellaterra 08193 Barcelona, Spain. +(3)Laboratory for Process Microbial Ecology and Bioinspirational Management +(PME&BIM), Technology Cluster Bioengineering Technology (CBeT), Campus De Nayer +Sint-Katelijne-Waver, KU Leuven, Jan De Nayerlaan 5, 2860 Sint-Katelijne-Waver, +Belgium; Technology Cluster Materials Technology, Campus Groep T, KU Leuven, +Andreas Vesaliusstraat 13 - Bus 2600, 3000 Leuven, Belgium. +(4)Laboratory for Process Microbial Ecology and Bioinspirational Management +(PME&BIM), Technology Cluster Bioengineering Technology (CBeT), Campus De Nayer +Sint-Katelijne-Waver, KU Leuven, Jan De Nayerlaan 5, 2860 Sint-Katelijne-Waver, +Belgium. +(5)Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure +Links 653, 9000 Gent, Belgium; Research Group of Sustainable Energy, Air, and +Water Technology, Department of Bioscience Engineering, University of Antwerp, +Groenenborgerlaan 171, 2020 Antwerpen, Belgium. Electronic address: +siegfried.vlaeminck@uantwerpen.be. + +During long-term extra-terrestrial missions, food is limited and waste is +generated. By recycling valuable nutrients from this waste via regenerative life +support systems, food can be produced in space. Astronauts' urine can, for +instance, be nitrified by micro-organisms into a liquid nitrate fertilizer for +plant growth in space. Due to stringent conditions in space, microbial +communities need to be be defined (gnotobiotic); therefore, synthetic rather +than mixed microbial communities are preferred. For urine nitrification, +synthetic communities face challenges, such as from salinity, ureolysis, and +organics. In this study, a synthetic microbial community containing an AOB +(Nitrosomonas europaea), NOB (Nitrobacter winogradskyi), and three ureolytic +heterotrophs (Pseudomonas fluorescens, Acidovorax delafieldii, and Delftia +acidovorans) was compiled and evaluated for these challenges. In reactor 1, salt +adaptation of the ammonium-fed AOB and NOB co-culture was possible up to +45mScm-1, which resembled undiluted nitrified urine, while maintaining a +44±10mgNH4+-NL-1d-1 removal rate. In reactor 2, the nitrifiers and ureolytic +heterotrophs were fed with urine and achieved a 15±6mg NO3--NL-1d-1 production +rate for 1% and 10% synthetic and fresh real urine, respectively. Batch activity +tests with this community using fresh real urine even reached 29±3mgNL-1d-1. +Organics removal in the reactor (69±15%) should be optimized to generate a +nitrate fertilizer for future space applications. + +Copyright © 2019 Elsevier GmbH. All rights reserved. + +DOI: 10.1016/j.syapm.2019.126021 +PMID: 31623889 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_32762153.txt b/references_cache/pmid_32762153.txt new file mode 100644 index 00000000..b0af9d32 --- /dev/null +++ b/references_cache/pmid_32762153.txt @@ -0,0 +1,38 @@ +1. Microb Biotechnol. 2021 Mar;14(2):488-502. doi: 10.1111/1751-7915.13640. Epub +2020 Aug 6. + +Synthetic community with six Pseudomonas strains screened from garlic +rhizosphere microbiome promotes plant growth. + +Zhuang L(1), Li Y(1), Wang Z(1), Yu Y(1), Zhang N(1), Yang C(1), Zeng Q(1), Wang +Q(1). + +Author information: +(1)Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green +Management, College of Plant Protection, China Agricultural University, Beijing, +100193, China. + +The rhizosphere microbiome plays an important role in the growth and health of +many plants, particularly for plant growth-promoting rhizobacteria (PGPR). +Although the use of PGPR could improve plant production, real-world applications +are still held back by low-efficiency methods of finding and using PGPR. In this +study, the structure of bacterial and fungal rhizosphere communities of Jinxiang +garlic under different growth periods (resume growth, bolting and maturation), +soil types (loam, sandy loam and sandy soil) and agricultural practices (with +and without microbial products) were explored by using amplicon sequencing. +High-efficiency top-down approaches based on high-throughput technology and +synthetic community (SynCom) approaches were used to find PGPR in garlic +rhizosphere and improve plant production. Our findings indicated that +Pseudomonas was a key PGPR in the rhizosphere of garlic. Furthermore, SynCom +with six Pseudomonas strains isolated from the garlic rhizosphere were +constructed, which showed that they have the ability to promote plant growth. + +© 2020 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd +and Society for Applied Microbiology. + +DOI: 10.1111/1751-7915.13640 +PMCID: PMC7936309 +PMID: 32762153 [Indexed for MEDLINE] + +Conflict of interest statement: None of the authors have any conflict of +interest. \ No newline at end of file diff --git a/references_cache/pmid_32788711.txt b/references_cache/pmid_32788711.txt new file mode 100644 index 00000000..37738642 --- /dev/null +++ b/references_cache/pmid_32788711.txt @@ -0,0 +1,47 @@ +1. ISME J. 2020 Nov;14(11):2816-2828. doi: 10.1038/s41396-020-00737-5. Epub 2020 +Aug 12. + +Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between +bacteria in a synthetic community. + +Fritts RK(1), Bird JT(2), Behringer MG(3), Lipzen A(4), Martin J(4), Lynch M(3), +McKinlay JB(5). + +Author information: +(1)Department of Biology, Indiana University, Bloomington, IN, 47405, USA. +(2)Department of Biochemistry and Molecular Biology, University of Arkansas for +Medical Sciences, Little Rock, AR, 72205, USA. +(3)School of Life Sciences, Biodesign Center for Mechanisms of Evolution, +Arizona State University, Tempe, AZ, 85281, USA. +(4)Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. +(5)Department of Biology, Indiana University, Bloomington, IN, 47405, USA. +jmckinla@indiana.edu. + +Interactive microbial communities are ubiquitous, influencing biogeochemical +cycles and host health. One widespread interaction is nutrient exchange, or +cross-feeding, wherein metabolites are transferred between microbes. Some +cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are +communally valuable and impose a cost on the producer. The mechanisms that +enforce cross-feeding of communally valuable metabolites are not fully +understood. Previously we engineered a cross-feeding coculture between N2-fixing +Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. +palustris excretes essential nitrogen as NH4+ to E. coli, while E. coli excretes +essential carbon as fermentation products to R. palustris. Here, we sought to +determine whether a reciprocal cross-feeding relationship would evolve +spontaneously in cocultures with wild-type R. palustris, which is not known to +excrete NH4+. Indeed, we observed the emergence of NH4+ cross-feeding, but +driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a +regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+ +transporter. This activity likely allowed E. coli to subsist on the small amount +of leaked NH4+ and better reciprocate through elevated excretion of fermentation +products from a larger E. coli population. Our results indicate that enhanced +nutrient uptake by recipients, rather than increased excretion by producers, is +an underappreciated yet possibly prevalent mechanism by which cross-feeding can +emerge. + +DOI: 10.1038/s41396-020-00737-5 +PMCID: PMC7784955 +PMID: 32788711 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare that they have no conflict +of interest. \ No newline at end of file diff --git a/references_cache/pmid_34745050.txt b/references_cache/pmid_34745050.txt new file mode 100644 index 00000000..0391c1ee --- /dev/null +++ b/references_cache/pmid_34745050.txt @@ -0,0 +1,46 @@ +1. Front Microbiol. 2021 Oct 21;12:747541. doi: 10.3389/fmicb.2021.747541. +eCollection 2021. + +Modulating Drought Stress Response of Maize by a Synthetic Bacterial Community. + +Armanhi JSL(1)(2), de Souza RSC(1)(2), Biazotti BB(1)(2)(3), Yassitepe +JECT(2)(4), Arruda P(1)(2)(3). + +Author information: +(1)Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de +Campinas (UNICAMP), Campinas, Brazil. +(2)Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de +Campinas (UNICAMP), Campinas, Brazil. +(3)Departamento de Genética e Evolução, Instituto de Biologia, Universidade +Estadual de Campinas (UNICAMP), Campinas, Brazil. +(4)Embrapa Informática Agropecuária, Campinas, Brazil. + +Plant perception and responses to environmental stresses are known to encompass +a complex set of mechanisms in which the microbiome is involved. Knowledge about +plant physiological responses is therefore critical for understanding the +contribution of the microbiome to plant resilience. However, as plant growth is +a dynamic process, a major hurdle is to find appropriate tools to effectively +measure temporal variations of different plant physiological parameters. Here, +we used a non-invasive real-time phenotyping platform in a one-to-one +(plant-sensors) set up to investigate the impact of a synthetic community +(SynCom) harboring plant-beneficial bacteria on the physiology and response of +three commercial maize hybrids to drought stress (DS). SynCom inoculation +significantly reduced yield loss and modulated vital physiological traits. +SynCom-inoculated plants displayed lower leaf temperature, reduced turgor loss +under severe DS and a faster recovery upon rehydration, likely as a result of +sap flow modulation and better water usage. Microbiome profiling revealed that +SynCom bacterial members were able to robustly colonize mature plants and +recruit soil/seed-borne beneficial microbes. The high-resolution temporal data +allowed us to record instant plant responses to daily environmental +fluctuations, thus revealing the impact of the microbiome in modulating maize +physiology, resilience to drought, and crop productivity. + +Copyright © 2021 Armanhi, de Souza, Biazotti, Yassitepe and Arruda. + +DOI: 10.3389/fmicb.2021.747541 +PMCID: PMC8566980 +PMID: 34745050 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_35444261.txt b/references_cache/pmid_35444261.txt new file mode 100644 index 00000000..5ad0d03b --- /dev/null +++ b/references_cache/pmid_35444261.txt @@ -0,0 +1,56 @@ +1. ISME J. 2022 Aug;16(8):1907-1920. doi: 10.1038/s41396-022-01238-3. Epub 2022 +Apr 20. + +Synthetic bacterial community derived from a desert rhizosphere confers salt +stress resilience to tomato in the presence of a soil microbiome. + +Schmitz L(#)(1), Yan Z(#)(1), Schneijderberg M(1), de Roij M(1), Pijnenburg +R(1), Zheng Q(1), Franken C(1), Dechesne A(2), Trindade LM(2), van Velzen R(3), +Bisseling T(1), Geurts R(4), Cheng X(5)(6). + +Author information: +(1)Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, +Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, +Wageningen, The Netherlands. +(2)Laboratory of Plant Breeding, Plant Sciences Group, Wageningen University & +Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. +(3)Biosystematics, Plant Sciences Group, Wageningen University & Research, +Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. +(4)Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, +Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, +Wageningen, The Netherlands. rene.geurts@wur.nl. +(5)Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, +Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, +Wageningen, The Netherlands. xu.cheng@wur.nl. +(6)Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome +Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics +Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, +China. xu.cheng@wur.nl. +(#)Contributed equally + +The root bacterial microbiome is important for the general health of the plant. +Additionally, it can enhance tolerance to abiotic stresses, exemplified by plant +species found in extreme ecological niches like deserts. These complex +microbe-plant interactions can be simplified by constructing synthetic bacterial +communities or SynComs from the root microbiome. Furthermore, SynComs can be +applied as biocontrol agents to protect crops against abiotic stresses such as +high salinity. However, there is little knowledge on the design of a SynCom that +offers a consistent protection against salt stress for plants growing in a +natural and, therefore, non-sterile soil which is more realistic to an +agricultural setting. Here we show that a SynCom of five bacterial strains, +originating from the root of the desert plant Indigofera argentea, protected +tomato plants growing in a non-sterile substrate against a high salt stress. +This phenotype correlated with the differential expression of salt stress +related genes and ion accumulation in tomato. Quantification of the SynCom +strains indicated a low penetrance into the natural soil used as the non-sterile +substrate. Our results demonstrate how a desert microbiome could be engineered +into a simplified SynCom that protected tomato plants growing in a natural soil +against an abiotic stress. + +© 2022. The Author(s). + +DOI: 10.1038/s41396-022-01238-3 +PMCID: PMC9296610 +PMID: 35444261 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no competing interests. \ No newline at end of file diff --git a/references_cache/pmid_35869094.txt b/references_cache/pmid_35869094.txt new file mode 100644 index 00000000..a552fb79 --- /dev/null +++ b/references_cache/pmid_35869094.txt @@ -0,0 +1,38 @@ +7. NPJ Biofilms Microbiomes. 2022 Jul 22;8(1):61. doi: +10.1038/s41522-022-00322-y. + +Synthetic periphyton as a model system to understand species dynamics in complex +microbial freshwater communities. + +Lamprecht O(1), Wagner B(1), Derlon N(1), Tlili A(2). + +Author information: +(1)Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, +Switzerland. +(2)Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, +Switzerland. ahmed.tlili@eawag.ch. + +Phototrophic biofilms, also known as periphyton, are microbial freshwater +communities that drive crucial ecological processes in streams and lakes. +Gaining a deep mechanistic understanding of the biological processes occurring +in natural periphyton remains challenging due to the high complexity and +variability of such communities. To address this challenge, we rationally +developed a workflow to construct a synthetic community by co-culturing 26 +phototrophic species (i.e., diatoms, green algae, and cyanobacteria) that were +inoculated in a successional sequence to create a periphytic biofilm on glass +slides. We show that this community is diverse, stable, and highly reproducible +in terms of microbial composition, function, and 3D spatial structure of the +biofilm. We also demonstrate the ability to monitor microbial dynamics at the +single species level during periphyton development and how their abundances are +impacted by stressors such as increased temperature and a herbicide, singly and +in combination. Overall, such a synthetic periphyton, grown under controlled +conditions, can be used as a model system for theory testing through targeted +manipulation. + +© 2022. The Author(s). + +DOI: 10.1038/s41522-022-00322-y +PMCID: PMC9307524 +PMID: 35869094 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no competing interests. diff --git a/references_cache/pmid_35992653.txt b/references_cache/pmid_35992653.txt new file mode 100644 index 00000000..370dae46 --- /dev/null +++ b/references_cache/pmid_35992653.txt @@ -0,0 +1,54 @@ +1. Front Microbiol. 2022 Aug 5;13:967885. doi: 10.3389/fmicb.2022.967885. +eCollection 2022. + +Designing a synthetic microbial community devoted to biological control: The +case study of Fusarium wilt of banana. + +Prigigallo MI(1), Gómez-Lama Cabanás C(2), Mercado-Blanco J(2), Bubici G(1). + +Author information: +(1)Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale +delle Ricerche, Bari, Italy. +(2)Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, +Agencia Estatal Consejo Superior de Investigaciones Científicas, Córdoba, Spain. + +Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (TR4) is threatening +banana production because of its increasing spread. Biological control +approaches have been widely studied and constitute interesting complementary +measures to integrated disease management strategies. They have been based +mainly on the use of single biological control agents (BCAs). In this study, we +moved a step forward by designing a synthetic microbial community (SynCom) for +the control of Fusarium wilt of banana (FWB). Ninety-six isolates of Pseudomonas +spp., Bacillus spp., Streptomyces spp., and Trichoderma spp. were obtained from +the banana rhizosphere and selected in vitro for the antagonism against Foc TR4. +In pot experiments, a large community such as SynCom 1.0 (44 isolates with +moderate to high antagonistic activity) or a small one such as SynCom 1.1 (seven +highly effective isolates) provided similar disease control (35% symptom +severity reduction). An in vitro study of the interactions among SynCom 1.1 +isolates and between them and Foc revealed that beneficial microorganisms not +only antagonized the pathogen but also some of the SynCom constituents. +Furthermore, Foc defended itself by antagonizing the beneficial microbes. We +also demonstrated that fusaric acid, known as one of the secondary metabolites +of Fusarium species, might be involved in such an interaction. With this +knowledge, SynCom 1.2 was then designed with three isolates: Pseudomonas +chlororaphis subsp. piscium PS5, Bacillus velezensis BN8.2, and Trichoderma +virens T2C1.4. A non-simultaneous soil application of these isolates (to +diminish cross-inhibition) delayed FWB progress over time, with significant +reductions in incidence and severity. SynCom 1.2 also performed better than two +commercial BCAs, BioPak® and T-Gro. Eventually, SynCom 1.2 isolates were +characterized for several biocontrol traits and their genome was sequenced. Our +data showed that assembling a SynCom for biocontrol is not an easy task. The +mere mixtures of antagonists (e.g., SynCom 1.0 and 1.1) might provide effective +biocontrol, but an accurate investigation of the interactions among beneficial +microorganisms is needed to improve the results (e.g., SynCom 1.2). SynCom 1.2 +is a valuable tool to be further developed for the biological control of FWB. + +Copyright © 2022 Prigigallo, Gómez-Lama Cabanás, Mercado-Blanco and Bubici. + +DOI: 10.3389/fmicb.2022.967885 +PMCID: PMC9389584 +PMID: 35992653 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_36070752.txt b/references_cache/pmid_36070752.txt new file mode 100644 index 00000000..c2b7c2e2 --- /dev/null +++ b/references_cache/pmid_36070752.txt @@ -0,0 +1,71 @@ +1. Cell. 2022 Sep 15;185(19):3617-3636.e19. doi: 10.1016/j.cell.2022.08.003. Epub + 2022 Sep 6. + +Design, construction, and in vivo augmentation of a complex gut microbiome. + +Cheng AG(1), Ho PY(2), Aranda-Díaz A(2), Jain S(3), Yu FB(4), Meng X(4), Wang +M(5), Iakiviak M(6), Nagashima K(6), Zhao A(6), Murugkar P(7), Patil A(6), +Atabakhsh K(6), Weakley A(4), Yan J(3), Brumbaugh AR(6), Higginbottom S(6), +Dimas A(6), Shiver AL(2), Deutschbauer A(8), Neff N(3), Sonnenburg JL(9), Huang +KC(10), Fischbach MA(11). + +Author information: +(1)Department of Gastroenterology & Hepatology, Stanford School of Medicine, +Stanford, CA 94305, USA. Electronic address: alicec2@stanford.edu. +(2)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. +(3)Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. +(4)Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, +Stanford University, Stanford, CA 94305, USA. +(5)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; +Department of Microbiology and Immunology, Stanford University School of +Medicine, Stanford University, Stanford, CA 94305, USA. +(6)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; +ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of +Microbiology and Immunology, Stanford University School of Medicine, Stanford +University, Stanford, CA 94305, USA. +(7)ChEM-H Institute, Stanford University, Stanford, CA 94305, USA. +(8)Environmental Genomics and Systems Biology Division, Lawrence Berkeley +National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial +Biology, University of California, Berkeley, Berkeley, CA 94720, USA. +(9)Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of +Microbiology and Immunology, Stanford University School of Medicine, Stanford +University, Stanford, CA 94305, USA. +(10)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; +Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford +University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, +Stanford University School of Medicine, Stanford University, Stanford, CA 94305, +USA. Electronic address: kchuang@stanford.edu. +(11)Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; +Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford +University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, +Stanford University School of Medicine, Stanford University, Stanford, CA 94305, +USA. Electronic address: fischbach@fischbachgroup.org. + +Efforts to model the human gut microbiome in mice have led to important insights +into the mechanisms of host-microbe interactions. However, the model communities +studied to date have been defined or complex, but not both, limiting their +utility. Here, we construct and characterize in vitro a defined community of 104 +bacterial species composed of the most common taxa from the human gut microbiota +(hCom1). We then used an iterative experimental process to fill open niches: +germ-free mice were colonized with hCom1 and then challenged with a human fecal +sample. We identified new species that engrafted following fecal challenge and +added them to hCom1, yielding hCom2. In gnotobiotic mice, hCom2 exhibited +increased stability to fecal challenge and robust colonization resistance +against pathogenic Escherichia coli. Mice colonized by either hCom2 or a human +fecal community are phenotypically similar, suggesting that this consortium will +enable a mechanistic interrogation of species and genes on microbiome-associated +phenotypes. + +Copyright © 2022 Elsevier Inc. All rights reserved. + +DOI: 10.1016/j.cell.2022.08.003 +PMCID: PMC9691261 +PMID: 36070752 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of interests Stanford University and +the Chan Zuckerberg Biohub have patents pending for microbiome technologies on +which the authors are co-inventors. M.A.F. is a co-founder and director of +Federation Bio and Kelonia, a co-founder of Revolution Medicines, and a member +of the scientific advisory boards of NGM Bio and Zymergen. A.G.C. and K.N. have +been paid consultants to Federation Bio. A.R.B. has been an employee of +Federation Bio. \ No newline at end of file diff --git a/references_cache/pmid_36472419.txt b/references_cache/pmid_36472419.txt new file mode 100644 index 00000000..58328e44 --- /dev/null +++ b/references_cache/pmid_36472419.txt @@ -0,0 +1,60 @@ +1. mSystems. 2022 Dec 20;7(6):e0095122. doi: 10.1128/msystems.00951-22. Epub 2022 + Dec 6. + +A Reproducible and Tunable Synthetic Soil Microbial Community Provides New +Insights into Microbial Ecology. + +Coker J(1), Zhalnina K(2), Marotz C(1), Thiruppathy D(3), Tjuanta M(3), D'Elia +G(3), Hailu R(3), Mahosky T(3), Rowan M(3), Northen TR(2)(4), Zengler +K(1)(3)(5). + +Author information: +(1)Department of Pediatrics, University of California, San Diego, La Jolla, +California, USA. +(2)Environmental Genomics and Systems Biology Division, Berkeley Lab, Berkeley, +California, USA. +(3)Department of Bioengineering, University of California, San Diego, La Jolla, +California, USA. +(4)The DOE Joint Genome Institute, Berkeley Lab, Berkeley, California, USA. +(5)Center for Microbiome Innovation, University of California, San Diego, La +Jolla, California, USA. + +Microbial soil communities form commensal relationships with plants to promote +the growth of both parties. The optimization of plant-microbe interactions to +advance sustainable agriculture is an important field in agricultural research. +However, investigation in this field is hindered by a lack of model microbial +community systems and efficient approaches for building these communities. Two +key challenges in developing standardized model communities are maintaining +community diversity over time and storing/resuscitating these communities after +cryopreservation, especially considering the different growth rates of +organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms +commonly found in the rhizosphere of diverse plant species, isolated from soil +surrounding a single switchgrass plant, has been developed and optimized for in +vitro experiments. The model soil community grows reproducibly between +replicates and experiments, with a high community α-diversity being achieved +through growth in low-nutrient media and through the adjustment of the starting +composition ratios for the growth of individual organisms. The community can +additionally be cryopreserved with glycerol, allowing for easy replication and +dissemination of this in vitro system. Furthermore, the SynCom also grows +reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the +application of this community to an existing in vitro plant-microbe system. +EcoFABs allow reproducible research in model plant systems, offering the precise +control of environmental conditions and the easy measurement of plant microbe +metrics. Our results demonstrate the generation of a stable and diverse +microbial SynCom for the rhizosphere that can be used with EcoFAB devices and +can be shared between research groups for maximum reproducibility. IMPORTANCE +Microbes associate with plants in distinct soil communities to the benefit of +both the soil microbes and the plants. Interactions between plants and these +microbes can improve plant growth and health and are therefore a field of study +in sustainable agricultural research. In this study, a model community of 16 +soil bacteria has been developed to further the reproducible study of plant-soil +microbe interactions. The preservation of the microbial community has been +optimized for dissemination to other research settings. Overall, this work will +advance soil microbe research through the optimization of a robust, reproducible +model community. + +DOI: 10.1128/msystems.00951-22 +PMCID: PMC9765266 +PMID: 36472419 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_36532452.txt b/references_cache/pmid_36532452.txt new file mode 100644 index 00000000..2d7f5957 --- /dev/null +++ b/references_cache/pmid_36532452.txt @@ -0,0 +1,48 @@ +1. Front Microbiol. 2022 Dec 1;13:1074153. doi: 10.3389/fmicb.2022.1074153. +eCollection 2022. + +Stably transmitted defined microbial community in honeybees preserves Hafnia +alvei inhibition by regulating the immune system. + +Wang J(1), Lang H(1), Zhang W(2), Zhai Y(3)(4), Zheng L(3)(4), Chen H(3)(4), Liu +Y(3)(4), Zheng H(1). + +Author information: +(1)College of Food Science and Nutritional Engineering, China Agricultural +University, Beijing, China. +(2)Faculty of Agriculture and Food, Kunming University of Science and +Technology, Kunming, China. +(3)Shandong Academy of Agricultural Sciences, Institute of Plant Protection, +Jinan, China. +(4)Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural +Affairs, Jinan, China. + +The gut microbiota of honeybees is highly diverse at the strain level and +essential to the proper function and development of the host. Interactions +between the host and its gut microbiota, such as specific microbes regulating +the innate immune system, protect the host against pathogen infections. However, +little is known about the capacity of these strains deposited in one colony to +inhibit pathogens. In this study, we assembled a defined microbial community +based on phylogeny analysis, the 'Core-20' community, consisting of 20 strains +isolated from the honeybee intestine. The Core-20 community could trigger the +upregulation of immune gene expressions and reduce Hafnia alvei prevalence, +indicating immune priming underlies the microbial protective effect. Functions +related to carbohydrate utilization and the phosphoenolpyruvate-dependent sugar +phosphotransferase system (PTS systems) are represented in genomic analysis of +the defined community, which might be involved in manipulating immune responses. +Additionally, we found that the defined Core-20 community is able to colonize +the honeybee gut stably through passages. In conclusion, our findings highlight +that the synthetic gut microbiota could offer protection by regulating the host +immune system, suggesting that the strain collection can yield insights into +host-microbiota interactions and provide solutions to protect honeybees from +pathogen infections. + +Copyright © 2022 Wang, Lang, Zhang, Zhai, Zheng, Chen, Liu and Zheng. + +DOI: 10.3389/fmicb.2022.1074153 +PMCID: PMC9751035 +PMID: 36532452 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_36847519.txt b/references_cache/pmid_36847519.txt new file mode 100644 index 00000000..a16c8cff --- /dev/null +++ b/references_cache/pmid_36847519.txt @@ -0,0 +1,67 @@ +1. mBio. 2023 Apr 25;14(2):e0318922. doi: 10.1128/mbio.03189-22. Epub 2023 Feb +27. + +Cross-Feedings, Competition, and Positive and Negative Synergies in a +Four-Species Synthetic Community for Anaerobic Degradation of Cellulose to +Methane. + +Wang D(1), Hunt KA(2), Candry P(2), Tao X(1)(3), Wofford NQ(1), Zhou +J(1)(3)(4)(5)(6), McInerney MJ(1), Stahl DA(2), Tanner RS(1), Zhou A(1)(3), +Winkler M(2), Pan C(1)(6). + +Author information: +(1)Department of Microbiology and Plant Biology, University of Oklahoma, Norman, +Oklahoma, USA. +(2)Department of Civil and Environmental Engineering, University of Washington, +Seattle, Washington, USA. +(3)Institute for Environmental Genomics, University of Oklahoma, Norman, +Oklahoma, USA. +(4)School of Civil Engineering and Environmental Sciences, University of +Oklahoma, Norman, Oklahoma, USA. +(5)Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, +Berkeley, California, USA. +(6)School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA. + +Complex interactions exist among microorganisms in a community to carry out +ecological processes and adapt to changing environments. Here, we constructed a +quad-culture consisting of a cellulolytic bacterium (Ruminiclostridium +cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an +acetoclastic methanogen (Methanosaeta concilii), and a sulfate-reducing +bacterium (Desulfovibrio vulgaris). The four microorganisms in the quad-culture +cooperated via cross-feeding to produce methane using cellulose as the only +carbon source and electron donor. The community metabolism of the quad-culture +was compared with those of the R. cellulolyticum-containing tri-cultures, +bi-cultures, and mono-culture. Methane production was higher in the quad-culture +than the sum of the increases in the tri-cultures, which was attributed to a +positive synergy of four species. In contrast, cellulose degradation by the +quad-culture was lower than the additive effects of the tri-cultures which +represented a negative synergy. The community metabolism of the quad-culture was +compared between a control condition and a treatment condition with sulfate +addition using metaproteomics and metabolic profiling. Sulfate addition enhanced +sulfate reduction and decreased methane and CO2 productions. The cross-feeding +fluxes in the quad-culture in the two conditions were modeled using a community +stoichiometric model. Sulfate addition strengthened metabolic handoffs from R. +cellulolyticum to M. concilii and D. vulgaris and intensified substrate +competition between M. hungatei and D. vulgaris. Overall, this study uncovered +emergent properties of higher-order microbial interactions using a four-species +synthetic community. IMPORTANCE A synthetic community was designed using four +microbial species that together performed distinct key metabolic processes in +the anaerobic degradation of cellulose to methane and CO2. The microorganisms +exhibited expected interactions, such as cross-feeding of acetate from a +cellulolytic bacterium to an acetoclastic methanogen and competition of H2 +between a sulfate reducing bacterium and a hydrogenotrophic methanogen. This +validated our rational design of the interactions between microorganisms based +on their metabolic roles. More interestingly, we also found positive and +negative synergies as emergent properties of high-order microbial interactions +among three or more microorganisms in cocultures. These microbial interactions +can be quantitatively measured by adding and removing specific members. A +community stoichiometric model was constructed to represent the fluxes in the +community metabolic network. This study paved the way toward a more predictive +understanding of the impact of environmental perturbations on microbial +interactions sustaining geochemically significant processes in natural systems. + +DOI: 10.1128/mbio.03189-22 +PMCID: PMC10128006 +PMID: 36847519 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_37154752.txt b/references_cache/pmid_37154752.txt new file mode 100644 index 00000000..91f526ae --- /dev/null +++ b/references_cache/pmid_37154752.txt @@ -0,0 +1,60 @@ +1. Microbiol Spectr. 2023 Jun 15;11(3):e0452822. doi: 10.1128/spectrum.04528-22. +Epub 2023 May 8. + +Synthetic Denitrifying Communities Reveal a Positive and Dynamic +Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution. + +Wu B(1), Guan X(1), Deng T(1), Yang X(1), Li J(2), Zhou M(1), Wang C(1), Wang +S(1), Yan Q(1), Shu L(1), He Q(3), He Z(1)(2). + +Author information: +(1)Environmental Microbiomics Research Center, School of Environmental Science +and Engineering, Southern Marine Science and Engineering Guangdong Laboratory +(Zhuhai), Sun Yat-sen University, Guangzhou, China. +(2)College of Agronomy, Hunan Agricultural University, Changsha, China. +(3)Department of Civil and Environmental Engineering, The University of +Tennessee, Knoxville, Tennessee, USA. + +Biodiversity is vital for ecosystem functions and services, and many studies +have reported positive, negative, or neutral biodiversity-ecosystem functioning +(BEF) relationships in plant and animal systems. However, if the BEF +relationship exists and how it evolves remains elusive in microbial systems. +Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying +communities (SDCs) with a richness gradient spanning 1 to 12 species, which were +subjected to approximately 180 days (with 60 transfers) of experimental +evolution with generational changes in community functions continuously tracked. +A significant positive correlation was observed between community richness and +functions, represented by productivity (biomass) and denitrification rate, +however, such a positive correlation was transient, only significant in earlier +days (0 to 60) during the evolution experiment (180 days). Also, we found that +community functions generally increased throughout the evolution experiment. +Furthermore, microbial community functions with lower richness exhibited greater +increases than those with higher richness. Biodiversity effect analysis revealed +positive BEF relationships largely attributable to complementary effects, which +were more pronounced in communities with lower richness than those with higher +richness. This study is one of the first studies that advances our understanding +of BEF relationships and their evolutionary mechanisms in microbial systems, +highlighting the crucial role of evolution in predicting the BEF relationship in +microbial systems. IMPORTANCE Despite the consensus that biodiversity supports +ecosystem functioning, not all experimental models of macro-organisms support +this notion with positive, negative, or neutral biodiversity-ecosystem +functioning (BEF) relationships reported. The fast-growing, metabolically +versatile, and easy manipulation nature of microbial communities allows us to +explore well the BEF relationship and further interrogate if the BEF +relationship remains constant during long-term community evolution. Here, we +constructed multiple synthetic denitrifying communities (SDCs) by randomly +selecting species from a candidate pool of 12 Shewanella denitrifiers. These +SDCs differ in species richness, spanning 1 to 12 species, and were monitored +continuously for community functional shifts during approximately 180-day +parallel cultivation. We demonstrated that the BEF relationship was dynamic with +initially (day 0 to 60) greater productivity and denitrification among SDCs of +higher richness. However, such pattern was reversed thereafter with greater +productivity and denitrification increments in lower-richness SDCs, likely due +to a greater accumulation of beneficial mutations during the experimental +evolution. + +DOI: 10.1128/spectrum.04528-22 +PMCID: PMC10269844 +PMID: 37154752 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_37207729.txt b/references_cache/pmid_37207729.txt new file mode 100644 index 00000000..82ed88da --- /dev/null +++ b/references_cache/pmid_37207729.txt @@ -0,0 +1,56 @@ +1. Environ Res. 2023 Aug 15;231(Pt 2):116184. doi: 10.1016/j.envres.2023.116184. +Epub 2023 May 18. + +Synthetic phylogenetically diverse communities promote denitrification and +stability. + +Zhou M(1), Guan X(1), Deng T(1), Hu R(1), Qian L(1), Yang X(1), Wu B(1), Li +J(2), He Q(3), Shu L(1), Yan Q(4), He Z(5). + +Author information: +(1)Environmental Microbiomics Research Center, School of Environmental Science +and Engineering, Southern Marine Science and Engineering Guangdong Laboratory +(Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, +Guangzhou, 510006, China. +(2)College of Agronomy, Hunan Agricultural University, Changsha, 410128, China. +(3)Department of Civil and Environmental Engineering, The University of +Tennessee, Knoxville, TN, 37996, USA. +(4)Environmental Microbiomics Research Center, School of Environmental Science +and Engineering, Southern Marine Science and Engineering Guangdong Laboratory +(Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, +Guangzhou, 510006, China. Electronic address: yanqingyun@sml-zhuhai.cn. +(5)Environmental Microbiomics Research Center, School of Environmental Science +and Engineering, Southern Marine Science and Engineering Guangdong Laboratory +(Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, +Guangzhou, 510006, China; College of Agronomy, Hunan Agricultural University, +Changsha, 410128, China. Electronic address: hezhili@sml-zhuhai.cn. + +Denitrification is an important process of the global nitrogen cycle as some of +its intermediates are environmentally important or related to global warming. +However, how the phylogenetic diversity of denitrifying communities affects +their denitrification rates and temporal stability remains unclear. Here we +selected denitrifiers based on their phylogenetic distance to construct two +groups of synthetic denitrifying communities: one closely related (CR) group +with all strains from the genus Shewanella and the other distantly related (DR) +group with all constituents from different genera. All synthetic denitrifying +communities (SDCs) were experimentally evolved for 200 generations. The results +showed that high phylogenetic diversity followed by experimental evolution +promoted the function and stability of synthetic denitrifying communities. +Specifically, the productivity and denitrification rates were significantly +(P < 0.05) higher with Paracocus denitrificans as the dominant species (since +the 50th generation) in the DR community than those in the CR community. The DR +community also showed significantly (t = 7.119, df = 10, P < 0.001) higher +stability through overyielding and asynchrony of species fluctuations, and +showed more complementarity than the CR group during the experimental evolution. +This study has important implications for applying synthetic communities to +remediate environmental problems and mitigate greenhouse gas emissions. + +Copyright © 2023 Elsevier Inc. All rights reserved. + +DOI: 10.1016/j.envres.2023.116184 +PMID: 37207729 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_37217495.txt b/references_cache/pmid_37217495.txt new file mode 100644 index 00000000..54687381 --- /dev/null +++ b/references_cache/pmid_37217495.txt @@ -0,0 +1,78 @@ +1. Nat Commun. 2023 May 22;14(1):2919. doi: 10.1038/s41467-023-38346-3. + +Selenomonas sputigena acts as a pathobiont mediating spatial structure and +biofilm virulence in early childhood caries. + +Cho H(#)(1), Ren Z(#)(2), Divaris K(3)(4), Roach J(5)(6), Lin BM(1), Liu C(1), +Azcarate-Peril MA(6)(7), Simancas-Pallares MA(8), Shrestha P(8)(9), Orlenko +A(10), Ginnis J(8), North KE(9), Zandona AGF(11), Ribeiro AA(12), Wu D(13)(14), +Koo H(15)(16). + +Author information: +(1)Department of Biostatistics, Gillings School of Global Public Health, +University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. +(2)Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, +School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA. +(3)Division of Pediatric and Public Health, Adams School of Dentistry, +University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. +Kimon_Divaris@unc.edu. +(4)Department of Epidemiology, Gillings School of Public Health, University of +North Carolina at Chapel Hill, Chapel Hill, NC, USA. Kimon_Divaris@unc.edu. +(5)UNC Information Technology Services and Research Computing, University of +North Carolina at Chapel Hill, Chapel Hill, NC, USA. +(6)UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School +of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. +(7)Department of Medicine, Division of Gastroenterology and Hepatology, School +of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. +(8)Division of Pediatric and Public Health, Adams School of Dentistry, +University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. +(9)Department of Epidemiology, Gillings School of Public Health, University of +North Carolina at Chapel Hill, Chapel Hill, NC, USA. +(10)Artificial Intelligence Innovation Lab, Cedars-Sinai Medical Center, Los +Angeles, CA, USA. +(11)Department of Comprehensive Care, School of Dental Medicine, Tufts +University, Boston, MA, USA. +(12)Division of Diagnostic Sciences, Adams School of Dentistry, University of +North Carolina at Chapel Hill, Chapel Hill, NC, USA. +(13)Department of Biostatistics, Gillings School of Global Public Health, +University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. +did@email.unc.edu. +(14)Division of Oral and Craniofacial Health Sciences, Adams School of +Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. +did@email.unc.edu. +(15)Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, +School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA. +koohy@upenn.edu. +(16)Department of Orthodontics, School of Dental Medicine, University of +Pennsylvania, Philadelphia, PA, USA. koohy@upenn.edu. +(#)Contributed equally + +Streptococcus mutans has been implicated as the primary pathogen in childhood +caries (tooth decay). While the role of polymicrobial communities is +appreciated, it remains unclear whether other microorganisms are active +contributors or interact with pathogens. Here, we integrate multi-omics of +supragingival biofilm (dental plaque) from 416 preschool-age children (208 males +and 208 females) in a discovery-validation pipeline to identify disease-relevant +inter-species interactions. Sixteen taxa associate with childhood caries in +metagenomics-metatranscriptomics analyses. Using multiscale/computational +imaging and virulence assays, we examine biofilm formation dynamics, spatial +arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae +and Leptotrichia wadei, either individually or with S. mutans. We show that S. +sputigena, a flagellated anaerobe with previously unknown role in supragingival +biofilm, becomes trapped in streptococcal exoglucans, loses motility but +actively proliferates to build a honeycomb-like multicellular-superstructure +encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal +an unrecognized ability of S. sputigena to colonize supragingival tooth +surfaces. While incapable of causing caries on its own, when co-infected with S. +mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates +disease severity in vivo. In summary, we discover a pathobiont cooperating with +a known pathogen to build a unique spatial structure and heighten biofilm +virulence in a prevalent human disease. + +© 2023. The Author(s). + +DOI: 10.1038/s41467-023-38346-3 +PMCID: PMC10202936 +PMID: 37217495 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no competing interests. \ No newline at end of file diff --git a/references_cache/pmid_37275168.txt b/references_cache/pmid_37275168.txt new file mode 100644 index 00000000..01477337 --- /dev/null +++ b/references_cache/pmid_37275168.txt @@ -0,0 +1,60 @@ +1. Front Microbiol. 2023 May 19;14:1167839. doi: 10.3389/fmicb.2023.1167839. +eCollection 2023. + +Promotion of the growth and yield of Zea mays by synthetic microbial communities +from Jala maize. + +De la Vega-Camarillo E(1), Sotelo-Aguilar J(1), Rios-Galicia B(1), +Mercado-Flores Y(2), Arteaga-Garibay R(3), Villa-Tanaca L(1), +Hernández-Rodríguez C(1). + +Author information: +(1)Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de +Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico +Nacional, Ciudad de México, Mexico. +(2)Laboratorio de Aprovechamiento Integral de Recursos Bióticos, Universidad +Politécnica de Pachuca, Hidalgo, Mexico. +(3)Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos +Genéticos, INIFAP, Jalisco, Mexico. + +Plant growth-promoting bacteria (PGPB) are a source of nutrient supply, +stimulate plant growth, and even act in the biocontrol of phytopathogens. +However, these phenotypic traits have rarely been explored in culturable +bacteria from native maize landraces. In this study, synthetic microbial +communities (SynCom) were assembled with a set of PGPB isolated from the Jala +maize landrace, some of them with additional abilities for the biocontrol of +phytopathogenic fungi and the stimulation of plant-induced systemic resistance +(ISR). Three SynCom were designed considering the phenotypic traits of bacterial +strains, including Achromobacter xylosoxidans Z2K8, Burkholderia sp. Z1AL11, +Klebsiella variicola R3J3HD7, Kosakonia pseudosacchari Z2WD1, Pantoea ananatis +E2HD8, Pantoea sp. E2AD2, Phytobacter diazotrophicus Z2WL1, Pseudomonas +protegens E1BL2, and P. protegens E2HL9. Plant growth promotion in gnotobiotic +and greenhouse seedlings assays was performed with Conejo landrace; meanwhile, +open field tests were carried out on hybrid CPL9105W maize. In all experimental +models, a significant promotion of plant growth was observed. In gnotobiotic +assays, the roots and shoot length of the maize seedlings increased 4.2 and 3.0 +times, respectively, compared to the untreated control. Similarly, the sizes and +weights of the roots and shoots of the plants increased significantly in the +greenhouse assays. In the open field assay performed with hybrid CPL9105W maize, +the yield increased from 11 tons/ha for the control to 16 tons/ha inoculated +with SynCom 3. In addition, the incidence of rust fungal infections decreased +significantly from 12.5% in the control to 8% in the treatment with SynCom 3. +All SynCom designs promoted the growth of maize in all assays. However, SynCom 3 +formulated with A. xylosoxidans Z2K8, Burkholderia sp. Z1AL11, K. variicola +R3J3HD7, P. ananatis E2HD8, P. diazotrophicus Z2WL1, and P. protegens E1BL2 +displayed the best results for promoting plant growth, their yield, and the +inhibition of fungal rust. This study demonstrated the biotechnological +eco-friendly plant growth-promoting potential of SynCom assemblies with +culturable bacteria from native maize landraces for more sustainable and +economic agriculture. + +Copyright © 2023 De la Vega-Camarillo, Sotelo-Aguilar, Rios-Galicia, +Mercado-Flores, Arteaga-Garibay, Villa-Tanaca and Hernández-Rodríguez. + +DOI: 10.3389/fmicb.2023.1167839 +PMCID: PMC10235630 +PMID: 37275168 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_37299063.txt b/references_cache/pmid_37299063.txt new file mode 100644 index 00000000..9525a13f --- /dev/null +++ b/references_cache/pmid_37299063.txt @@ -0,0 +1,40 @@ +1. Plants (Basel). 2023 May 24;12(11):2083. doi: 10.3390/plants12112083. + +Nodule Synthetic Bacterial Community as Legume Biofertilizer under Abiotic +Stress in Estuarine Soils. + +Flores-Duarte NJ(1), Navarro-Torre S(1), Mateos-Naranjo E(2), Redondo-Gómez +S(2), Pajuelo E(1), Rodríguez-Llorente ID(1). + +Author information: +(1)Departamento de Microbiología y Parasitología, Universidad de Sevilla, 41012 +Seville, Spain. +(2)Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, 41012 +Seville, Spain. + +Estuaries are ecologically important ecosystems particularly affected by climate +change and human activities. Our interest is focused on the use of legumes to +fight against the degradation of estuarine soils and loss of fertility under +adverse conditions. This work was aimed to determine the potential of a nodule +synthetic bacterial community (SynCom), including two Ensifer sp. and two +Pseudomonas sp. strains isolated from Medicago spp. nodules, to promote M. +sativa growth and nodulation in degraded estuarine soils under several abiotic +stresses, including high metal contamination, salinity, drought and high +temperature. These plant growth promoting (PGP) endophytes were able to maintain +and even increase their PGP properties in the presence of metals. Inoculation +with the SynCom in pots containing soil enhanced plant growth parameters (from +3- to 12-fold increase in dry weight), nodulation (from 1.5- to 3-fold increase +in nodules number), photosynthesis and nitrogen content (up to 4-fold under +metal stress) under all the controlled conditions tested. The increase in plant +antioxidant enzymatic activities seems to be a common and important mechanism of +plant protection induced by the SynCom under abiotic stress conditions. The +SynCom increased M. sativa metals accumulation in roots, with low levels of +metals translocation to shoots. Results indicated that the SynCom used in this +work is an appropriate ecological and safe tool to improve Medicago growth and +adaptation to degraded estuarine soils under climate change conditions. + +DOI: 10.3390/plants12112083 +PMCID: PMC10255395 +PMID: 37299063 + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_37549573.txt b/references_cache/pmid_37549573.txt new file mode 100644 index 00000000..a595f654 --- /dev/null +++ b/references_cache/pmid_37549573.txt @@ -0,0 +1,59 @@ +1. Plant Physiol Biochem. 2023 Sep;202:107941. doi: 10.1016/j.plaphy.2023.107941. + Epub 2023 Aug 5. + +A simplified synthetic rhizosphere bacterial community steers plant oxylipin +pathways for preventing foliar phytopathogens. + +Huang J(1), Zhu L(2), Lu X(1), Cui F(3), Wang J(1), Zhou C(4). + +Author information: +(1)Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural +Affairs, Anhui Science and Technology University, Chuzhou 233100, China. +(2)Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural +Affairs, Anhui Science and Technology University, Chuzhou 233100, China; School +of Life Science and Technology, Tongji University, Shanghai 200092, China. +(3)Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural +Affairs, Anhui Science and Technology University, Chuzhou 233100, China. +Electronic address: cuif@ahstu.edu.cn. +(4)Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural +Affairs, Anhui Science and Technology University, Chuzhou 233100, China; Jiangsu +Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative +Innovation Center of Solid Organic Wastes, Educational Ministry Engineering +Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing +210095, China. Electronic address: zhoucheng@njau.edu.cn. + +Rhizosphere-enriched microbes induced by foliar phytopathogen infection can be +assembled into a functional community to enhance plant defense mechanisms. +However, the functions of stably-colonizing rhizosphere microbiota are rarely +investigated. In this study, Botrytis cinerea infection changed rhizosphere +bacterial communities in tomato plants. The phytopathogen-infected plants +recruited specific rhizosphere bacterial taxa, while several bacterial taxa +stably colonized the rhizosphere, regardless of phytopathogen infection. Through +the analysis of the rhizosphere bacterial community, we established a synthetic +community harboring 8 phytopathogen-inducible and 30 stably-colonizing bacteria +species. Furthermore, the 38-species community was simplified into a +three-species community, consisting of one phytopathogen-inducible +(Asticcacaulis sp.) and two stably-colonizing species (Arachidicoccus sp. And +Phenylobacterium sp.). The simplified community provided a durable protection +for the host plants by synergistic effects, with the phytopathogen-inducible +species triggering plant defense responses and the stably-colonizing species +promoting biofilm formation. The simplified community exhibited similar +protective effects as the 38-species community. Moreover, the activation of +oxylipin pathways in the phytopathogen-infected leaves was significantly +intensified by the simplified community. However, the inhibited biosynthesis of +antimicrobial divinyl ethers, including colneleic and colnelenic acid, fully +abolished the community-induced plant disease resistance. In contrast, +transgenic plants overexpressing SlLOX5 and SlDES1, with higher levels of +divinyl ethers, displayed stronger resistance against B. cinerea compared to +wild-type plants. Collectively, these findings provided insights into the +utilization of the simplified community for preventing gray mold disease. + +Copyright © 2023 Elsevier Masson SAS. All rights reserved. + +DOI: 10.1016/j.plaphy.2023.107941 +PMID: 37549573 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_37774801.txt b/references_cache/pmid_37774801.txt new file mode 100644 index 00000000..1de49022 --- /dev/null +++ b/references_cache/pmid_37774801.txt @@ -0,0 +1,48 @@ +1. Bioresour Technol. 2023 Dec;389:129799. doi: 10.1016/j.biortech.2023.129799. +Epub 2023 Sep 27. + +Construction of a synthetic microbial community based on multiomics linkage +technology and analysis of the mechanism of lignocellulose degradation. + +Chen J(1), Cai Y(1), Wang Z(1), Xu Z(1), Li J(1), Ma X(1), Zhuang W(2), Liu +D(2), Wang S(3), Song A(4), Xu J(1), Ying H(2). + +Author information: +(1)School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, +Zhengzhou 450001, China. +(2)School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, +Zhengzhou 450001, China; National Engineering Technique Research Center for +Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, +College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech +University, Nanjing 210009, China. +(3)School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, +Zhengzhou 450001, China. Electronic address: shileiwang@zzu.edu.cn. +(4)College of Life Science, Henan Agricultural University, 218 Ping An Avenue, +Zhengdong New District, Zhengzhou 450002, China. + +The efficient degradation of lignocellulose is a bottleneck for its integrated +utilization. This research performed species analysis and made functional +predictions in various ecosystems using multiomics coupling to construct a core +synthetic microbial community with efficient lignocellulose degradation +function. The synthetic microbial community was employed to degrade corn straw +via solid-state fermentation. The degradation mechanisms were resolved using +proteomics. The optimum culture conditions included 10% inoculum level (w/v), 4% +nitrogen source ratio and a fermentation time of 23 d. Under these conditions, +the degradation rates of cellulose, hemicellulose, and lignin were 34.91%, +45.94%, and 23.34%, respectively. Proteomic analysis revealed that lignin +1,4-β-xylanase, β-xylosidase and endo-1,4-β-xylanase were closely related to +lignocellulose degradation. The metabolic pathways involved in lignocellulose +degradation and the functional roles of eight strains were obtained. The +synthesis of a microbial community via multiomics linkage technology can +effectively decompose lignocellulose, which is useful for their further +utilization. + +Copyright © 2023 Elsevier Ltd. All rights reserved. + +DOI: 10.1016/j.biortech.2023.129799 +PMID: 37774801 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of Competing Interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_38277828.txt b/references_cache/pmid_38277828.txt new file mode 100644 index 00000000..6730c60a --- /dev/null +++ b/references_cache/pmid_38277828.txt @@ -0,0 +1,55 @@ +1. Water Res. 2024 Mar 1;251:121162. doi: 10.1016/j.watres.2024.121162. Epub 2024 + Jan 18. + +Deciphering the potential role of quorum quenching in efficient aerobic +denitrification driven by a synthetic microbial community. + +He Y(1), Yun H(2), Peng L(1), Ji J(1), Wang W(1), Li X(3). + +Author information: +(1)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou 730000, China. +(2)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou 730000, China; Gansu Key Laboratory of Biomonitoring and +Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou +University, Tianshui South Road #222, Lanzhou 730000, China. Electronic address: +yunh@lzu.edu.cn. +(3)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou 730000, China; Gansu Key Laboratory of Biomonitoring and +Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou +University, Tianshui South Road #222, Lanzhou 730000, China. Electronic address: +xkli@lzu.edu.cn. + +Low efficiency is one of the main challenges for the application of aerobic +denitrification technology in wastewater treatment. To improve denitrification +efficiency, a synthetic microbial community (SMC) composed of denitrifiers +Acinetobacter baumannii N1 (AC), Pseudomonas aeruginosa N2 (PA) and Aeromonas +hydrophila (AH) were constructed. The nitrate (NO3--N) reduction efficiency of +the SMC reached 97 % with little nitrite (NO2--N) accumulation, compared to the +single-culture systems and co-culture systems. In the SMC, AH proved to mainly +contribute to NO3--N reduction with the assistance of AC, while PA exerted +NO2--N reduction. AC and AH secreted N-hexanoyl-DL-homoserine lactone (C6-HSL) +to promote the electron transfer from the quinone pool to nitrate reductase. The +declined N-(3-oxododecanoyl)-L-homoserine lactone (3OC12-HSL), resulting from +quorum quenching (QQ) by AH, stimulated the excretion of pyocyanin, which could +improve the electron transfer from complex III to downstream denitrifying +enzymes for NO2--N reduction. In addition, C6-HSL mainly secreted by PA led to +the up-regulation of TCA cycle-related genes and provided sufficient energy +(such as NADH and ATP) for aerobic denitrification. In conclusion, members of +the SMC achieved efficient denitrification through the interactions between QQ, +electron transfer, and energy metabolism induced by N-acyl-homoserine lactones +(AHLs). This study provided a theoretical basis for the engineering application +of synthetic microbiome to remove nitrate wastewater. + +Copyright © 2024. Published by Elsevier Ltd. + +DOI: 10.1016/j.watres.2024.121162 +PMID: 38277828 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_38324131.txt b/references_cache/pmid_38324131.txt new file mode 100644 index 00000000..7f961b98 --- /dev/null +++ b/references_cache/pmid_38324131.txt @@ -0,0 +1,22 @@ +1. Sci China Life Sci. 2024 May;67(5):1085-1086. doi: 10.1007/s11427-024-2533-2. +Epub 2024 Feb 2. + +A synthetic microbial community used as a bioinoculant can overcome rice +production constraints in acid soils. + +O'Callaghan M(1), Shi S(2). + +Author information: +(1)Resilient Agriculture Group, AgResearch, Lincoln, Christcurch, 8140, New +Zealand. maureen.ocallaghan@agresearch.co.nz. +(2)Resilient Agriculture Group, AgResearch, Lincoln, Christcurch, 8140, New +Zealand. + +A customised synthetic microbial community (SynCom) composed of carefully +selected rhizosphere-competent bacterial strains improved rice growth, yield and +resistance to soil acidity and Al toxicity. + +© 2024. Science China Press. + +DOI: 10.1007/s11427-024-2533-2 +PMID: 38324131 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_38520150.txt b/references_cache/pmid_38520150.txt new file mode 100644 index 00000000..cd7e18fa --- /dev/null +++ b/references_cache/pmid_38520150.txt @@ -0,0 +1,35 @@ +1. J Appl Microbiol. 2024 Apr 1;135(4):lxae073. doi: 10.1093/jambio/lxae073. + +Seed-borne bacterial synthetic community resists seed pathogenic fungi and +promotes plant growth. + +Luo DL(1), Huang SY(1), Ma CY(1), Zhang XY(1), Sun K(1), Zhang W(1), Dai CC(1). + +Author information: +(1)Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu +Engineering and Technology and Research Center for Industrialization of +Microbial Resources, College of Life Sciences, Nanjing Normal University, +Nanjing, Jiangsu 210023, China. + +AIMS: In this study, the control effects of synthetic microbial communities +composed of peanut seed bacteria against seed aflatoxin contamination caused by +Aspergillus flavus and root rot by Fusarium oxysporum were evaluated. +METHODS AND RESULTS: Potentially conserved microbial synthetic communities (C), +growth-promoting synthetic communities (S), and combined synthetic communities +(CS) of peanut seeds were constructed after 16S rRNA Illumina sequencing, strain +isolation, and measurement of plant growth promotion indicators. Three synthetic +communities showed resistance to root rot and CS had the best effect after +inoculating into peanut seedlings. This was achieved by increased defense enzyme +activity and activated salicylic acid (SA)-related, systematically induced +resistance in peanuts. In addition, CS also inhibited the reproduction of A. +flavus on peanut seeds and the production of aflatoxin. These effects are +related to bacterial degradation of toxins and destruction of mycelia. +CONCLUSIONS: Inoculation with a synthetic community composed of seed bacteria +can help host peanuts resist the invasion of seeds by A. flavus and seedlings by +F. oxysporum and promote the growth of peanut seedlings. + +© The Author(s) 2024. Published by Oxford University Press on behalf of Applied +Microbiology International. + +DOI: 10.1093/jambio/lxae073 +PMID: 38520150 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_38748977.txt b/references_cache/pmid_38748977.txt new file mode 100644 index 00000000..6c5094d4 --- /dev/null +++ b/references_cache/pmid_38748977.txt @@ -0,0 +1,42 @@ +1. Environ Sci Technol. 2024 May 28;58(21):9446-9455. doi: +10.1021/acs.est.4c02789. Epub 2024 May 15. + +Construction of a Synthetic Microbial Community for Enzymatic Pretreatment of +Wheat Straw for Biogas Production via Anaerobic Digestion. + +Chen J(1), Cai Y(1)(2), Wang Z(1), Wang S(2), Li J(1), Song C(2), Zhuang +W(1)(3), Liu D(1)(3), Wang S(1), Song A(4), Xu J(1), Ying H(1)(3). + +Author information: +(1)School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, +Zhengzhou 450001, China. +(2)Luzhou LaoJiao Co., Ltd, Luzhou 646000, China. +(3)National Engineering Technique Research Center for Biotechnology, State Key +Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology +and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China. +(4)College of Life Science, Henan Agricultural University, 218 Ping An Avenue, +Zhengdong New District, Zhengzhou 450002, China. + +Biological pretreatment is a viable method for enhancing biogas production from +straw crops, with the improvement in lignocellulose degradation efficiency being +a crucial factor in this process. Herein, a metagenomic approach was used to +screen core microorganisms (Bacillus subtilis, Acinetobacter johnsonii, +Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading +abilities among samples from three environments: pile retting wheat straw (WS), +WS returned to soil, and forest soil. Subsequently, synthetic microbial +communities were constructed for fermentation-enzyme production. The crude +enzyme solution obtained was used to pretreat WS and was compared with two +commercial enzymes. The synthetic microbial community enzyme-producing +pretreatment (SMCEP) yielded the highest enzymatic digestion efficacy for WS, +yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99, +and 19.21%, respectively. Furthermore, pretreatment of WS with an enzyme +solution, followed by anaerobic digestion achieved satisfactory results. SMCEP +displayed the highest cumulative biogas production at 801.16 mL/g TS, which was +38.79% higher than that observed for WS, 22.15% higher than that of solid-state +commercial enzyme pretreatment and 25.41% higher than that of liquid commercial +enzyme pretreatment. These results indicate that enzyme-pretreated WS can +significantly enhance biogas production. This study represents a solution to the +environmental burden and energy use of crop residues. + +DOI: 10.1021/acs.est.4c02789 +PMID: 38748977 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_38840214.txt b/references_cache/pmid_38840214.txt new file mode 100644 index 00000000..f89486dc --- /dev/null +++ b/references_cache/pmid_38840214.txt @@ -0,0 +1,60 @@ +1. Microbiome. 2024 Jun 5;12(1):101. doi: 10.1186/s40168-024-01814-z. + +Synthetic community derived from grafted watermelon rhizosphere provides +protection for ungrafted watermelon against Fusarium oxysporum via microbial +synergistic effects. + +Qiao Y(1), Wang Z(1), Sun H(1), Guo H(1), Song Y(2), Zhang H(1), Ruan Y(1), Xu +Q(1)(3), Huang Q(1), Shen Q(1), Ling N(4)(5). + +Author information: +(1)Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab +for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, +210095, China. +(2)Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht +University, Padualaan 8, Utrecht, 3584 CH, the Netherlands. +(3)Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement +and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and +Technology, Lanzhou University, Lanzhou, 730020, China. +(4)Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab +for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, +210095, China. nling@njau.edu.cn. +(5)Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement +and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and +Technology, Lanzhou University, Lanzhou, 730020, China. nling@njau.edu.cn. + +BACKGROUND: Plant microbiota contributes to plant growth and health, including +enhancing plant resistance to various diseases. Despite remarkable progress in +understanding diseases resistance in plants, the precise role of rhizosphere +microbiota in enhancing watermelon resistance against soil-borne diseases +remains unclear. Here, we constructed a synthetic community (SynCom) of 16 core +bacterial strains obtained from the rhizosphere of grafted watermelon plants. We +further simplified SynCom and investigated the role of bacteria with synergistic +interactions in promoting plant growth through a simple synthetic community. +RESULTS: Our results demonstrated that the SynCom significantly enhanced the +growth and disease resistance of ungrafted watermelon grown in non-sterile soil. +Furthermore, analysis of the amplicon and metagenome data revealed the pivotal +role of Pseudomonas in enhancing plant health, as evidenced by a significant +increase in the relative abundance and biofilm-forming pathways of Pseudomonas +post-SynCom inoculation. Based on in vitro co-culture experiments and bacterial +metabolomic analysis, we selected Pseudomonas along with seven other members of +the SynCom that exhibited synergistic effects with Pseudomonas. It enabled us to +further refine the initially constructed SynCom into a simplified SynCom +comprising the eight selected bacterial species. Notably, the plant-promoting +effects of simplified SynCom were similar to those of the initial SynCom. +Furthermore, the simplified SynCom protected plants through synergistic effects +of bacteria. +CONCLUSIONS: Our findings suggest that the SynCom proliferate in the rhizosphere +and mitigate soil-borne diseases through microbial synergistic interactions, +highlighting the potential of synergistic effects between microorganisms in +enhancing plant health. This study provides a novel insight into using the +functional SynCom as a promising solution for sustainable agriculture. Video +Abstract. + +© 2024. The Author(s). + +DOI: 10.1186/s40168-024-01814-z +PMCID: PMC11151650 +PMID: 38840214 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no competing interests. \ No newline at end of file diff --git a/references_cache/pmid_39111313.txt b/references_cache/pmid_39111313.txt new file mode 100644 index 00000000..dda2a7eb --- /dev/null +++ b/references_cache/pmid_39111313.txt @@ -0,0 +1,58 @@ +1. Cell Rep Methods. 2024 Aug 19;4(8):100832. doi: 10.1016/j.crmeth.2024.100832. +Epub 2024 Aug 6. + +SkinCom, a synthetic skin microbial community, enables reproducible +investigations of the human skin microbiome. + +Lekbua A(1), Thiruppathy D(2), Coker J(3), Weng Y(4), Askarian F(3), Kousha +A(3), Marotz C(3), Hauw A(3), Nizet V(5), Zengler K(6). + +Author information: +(1)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; School of +Biological Sciences, University of California, San Diego, La Jolla, CA 92093, +USA. +(2)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; Department of +Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. +(3)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA. +(4)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and +Systems Biology Program, University of California, San Diego, La Jolla, CA +92093, USA. +(5)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; Glycobiology +Research and Training Center, University of California, San Diego, La Jolla, CA +92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of +California, San Diego, La Jolla, CA 92093, USA. +(6)Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, +University of California, San Diego, La Jolla, CA 92093, USA; Department of +Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; +Center for Microbiome Innovation, University of California, San Diego, La Jolla, +CA 92093, USA; Program in Materials Science and Engineering, University of +California, San Diego, La Jolla, CA 92093, USA. Electronic address: +kzengler@ucsd.edu. + +Existing models of the human skin have aided our understanding of skin health +and disease. However, they currently lack a microbial component, despite +microbes' demonstrated connections to various skin diseases. Here, we present a +robust, standardized model of the skin microbial community (SkinCom) to support +in vitro and in vivo investigations. Our methods lead to the formation of an +accurate, reproducible, and diverse community of aerobic and anaerobic bacteria. +Subsequent testing of SkinCom on the dorsal skin of mice allowed for DNA and RNA +recovery from both the applied SkinCom and the dorsal skin, highlighting its +practicality for in vivo studies and -omics analyses. Furthermore, 66% of the +responses to common cosmetic chemicals in vitro were in agreement with a human +trial. Therefore, SkinCom represents a valuable, standardized tool for +investigating microbe-metabolite interactions and facilitates the experimental +design of in vivo studies targeting host-microbe relationships. + +Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved. + +DOI: 10.1016/j.crmeth.2024.100832 +PMCID: PMC11384088 +PMID: 39111313 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of interests The authors declare no +competing interests. \ No newline at end of file diff --git a/references_cache/pmid_39345197.txt b/references_cache/pmid_39345197.txt new file mode 100644 index 00000000..64a647d0 --- /dev/null +++ b/references_cache/pmid_39345197.txt @@ -0,0 +1,58 @@ +1. Microbiol Spectr. 2024 Nov 5;12(11):e0431823. doi: 10.1128/spectrum.04318-23. +Epub 2024 Sep 30. + +Veillonella parvula acts as a pathobiont promoting the biofilm virulence and +cariogenicity of Streptococcus mutans in adult severe caries. + +Wei Y(#)(1), Zhang Y(#)(1), Zhuang Y(1), Tang Y(1), Nie H(1), Haung Y(2), Liu +T(2), Yang W(3), Yan F(1), Zhu Y(1). + +Author information: +(1)Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, +Institute of Stomatology, Nanjing University, Nanjing, China. +(2)Department of Endodontics, Nanjing Stomatological Hospital, Affiliated +Hospital of Medical School, Institute of Stomatology, Nanjing University, +Nanjing, China. +(3)Department of General Dentistry, Nanjing Stomatological Hospital, Affiliated +Hospital of Medical School, Institute of Stomatology, Nanjing University, +Nanjing, China. +(#)Contributed equally + +Adult severe caries (ASC) brings severe oral dysfunction and treatment +difficulties to patients, and yet no clear pathogenic mechanism for it has been +found. This study is focused on the composition of dental plaque microbiome +profiles in order to identify disease-relevant species and to investigate into +their interactions with the S. mutans. Samples of dental plaque were collected +for metagenomic analysis. The acidification, aciduricity, oxidative stress +tolerance, and gtf (glucosyltransferase) gene expression of S. mutans cocultured +with V. parvula which was identified as ASC-related dominant bacterium. The +biofilm formation and extracellular exopolysaccharide (EPS) synthesis of +dual-strain were analyzed with scanning electron microscopy (SEM), crystal +violet (CV) staining, live/dead bacterial staining, and confocal laser scanning +microscopy (CLSM). Furthermore, rodent model experiments were performed to +validate the in vivo cariogenicity of the dual-species biofilm. The most +significantly abundant taxon found associated with ASC was V. parvula. In vitro +experiments found that V. parvula can effectively promote S. mutans mature +biofilm formation with enhanced acid resistance, hydrogen peroxide detoxicity, +and biofilm virulence. Rodent model experiments revealed that V. parvula was +incapable of causing disease on its own, but it significantly heightened the +biofilm virulence of S. mutans when being co-infected and augmented the +progression, quantity, and severity of dental caries. Our findings demonstrated +that V. parvula may act as a synergistic pathobiont to modulate the metabolic +activity, spatial structure, and pathogenicity of biofilms of S. mutans in the +context of ASC.IMPORTANCEAdult severe caries (ASC), as a special type of acute +caries, is rarely reported and its worthiness of further study is still in +dispute. Yet studies on the etiology of severe caries in adults have not found a +clear pathogenic mechanism for it. Knowledge of the oral microbiota is important +for the treatment of dental caries. We discovered that the interaction between +V. parvula and S. mutans augments the severity of dental caries in vivo, +suggesting V. parvula may act as a synergistic pathobiont exacerbating biofilm +virulence of S. mutans in ASC. Our findings may improve the understanding of ASC +pathogenesis and are likely to provide a basis for planning appropriate +therapeutic strategies. + +DOI: 10.1128/spectrum.04318-23 +PMCID: PMC11537095 +PMID: 39345197 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_39481489.txt b/references_cache/pmid_39481489.txt new file mode 100644 index 00000000..990d5998 --- /dev/null +++ b/references_cache/pmid_39481489.txt @@ -0,0 +1,58 @@ +1. Chemosphere. 2024 Nov;367:143650. doi: 10.1016/j.chemosphere.2024.143650. Epub + 2024 Nov 1. + +A synthetic bacterial community engineered from Miscanthus floridulus roots +enhances ammonia nitrogen removal in ionic rare earth mine tailings. + +Zhaoyu K(1), Ye J(1), Pei K(1), He Y(1), Wang B(1), Huang S(1), Cai Q(1), Liu +Y(1), Ge G(2), Wu L(3). + +Author information: +(1)School of Life Science, Key Laboratory of Poyang Lake Environment and +Resource Utilization, Ministry of Education, Nanchang University, Nanchang, +330022, China. +(2)School of Life Science, Key Laboratory of Poyang Lake Environment and +Resource Utilization, Ministry of Education, Nanchang University, Nanchang, +330022, China. Electronic address: gge@ncu.edu.cn. +(3)School of Life Science, Key Laboratory of Poyang Lake Environment and +Resource Utilization, Ministry of Education, Nanchang University, Nanchang, +330022, China. Electronic address: ncusk724@hotmail.com. + +Ammonium sulfate, as the primary leaching agent, has caused significant nitrogen +pollution in rare earth elements (REEs) mining areas. Phytoremediation is a +promising remediation method, relying on the synergistic relationships between +plants and their root-associated microbiome. Nevertheless, harnessing the +microbiome to accelerate nitrogen transformation and absorption by plants is +challenging. Here, we investigated the composition, activities and culturable +fraction of the root bacterial microbiome of the pioneer plant Miscanthus +floridulus grown in a REEs tailing soil containing a high ammonia nitrogen (AN) +concentration at 344.35 mg kg-1. Based on this, we constructed a simplified +synthetic microbial community (SynCom) derived from the roots of M. floridulus, +possessing nitrification and denitrification capabilities, to help REEs mine +plants efficiently convert pollutant AN into nutrients, thereby enhancing plant +growth and AN removal. This SynCom, consisting of 10 bacterial strains, included +species of the genera Burkholderia (5) Paraburkholderia (1), Curtobacterium (1), +Leifsonia (1) and Sinomonas (2). As a result, this SynCom alone achieved a +significant reduction of 24.8% in AN content in tailing soil. When the SynCom +inoculated with plants, the reduction in AN was even more significant (32.6%), +surpassing the reduction achieved solely by plants (25.5%). Moreover, live +SynCom inoculation significantly increased shoot and root biomass by 39.8% and +49.7%, respectively, compared to dead SynCom inoculation. These results indicate +that the reduction in AN can be attributed to the SynCom's nitrification and +denitrification capabilities, as well as its ability to enhance plant nitrogen +absorption by stimulating their growth. Notably, seven nitrifying and +denitrifying strains of the SynCom are particularly enriched, suggesting that +plant roots selectively recruit nitrogen cycle-related bacteria to accelerate +nitrogen transformation and absorption. These results provide a practical +solution for harnessing the synergistic relationships between plants and their +root microbiome in environmental remediation efforts. + +Copyright © 2024 Elsevier Ltd. All rights reserved. + +DOI: 10.1016/j.chemosphere.2024.143650 +PMID: 39481489 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_39684532.txt b/references_cache/pmid_39684532.txt new file mode 100644 index 00000000..52ee27dc --- /dev/null +++ b/references_cache/pmid_39684532.txt @@ -0,0 +1,47 @@ +1. Int J Mol Sci. 2024 Nov 28;25(23):12819. doi: 10.3390/ijms252312819. + +Synthetic Microbial Community Isolated from Intercropping System Enhances P +Uptake in Rice. + +Ma H(1), Zhang H(1), Zheng C(2), Liu Z(1), Wang J(3)(4), Tian P(1), Wu Z(1), +Zhang H(5). + +Author information: +(1)Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China. +(2)ISPA, INRAE, F-33140 Villenave d'Ornon, France. +(3)State Key Laboratory of Vegetation and Environmental Change, Institute of +Botany, Chinese Academy of Sciences, Beijing 100093, China. +(4)China National Botanical Garden, Beijing 100093, China. +(5)Institute of Soil and Water Resources and Environmental Science, College of +Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of +Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, +China. + +Changes in root traits and rhizosphere microbiome are important ways to optimize +plant phosphorus (P) efficiency and promote multifunctionality in intercropping. +However, whether and how synthetic microbial communities isolated from +polyculture systems can facilitate plant growth and P uptake are still largely +unknown. A field experiment was first carried out to assess the rice yield and P +uptake in the rice/soybean intercropping systems, and a synthetic microbial +community (SynCom) isolated from intercropped rice was then constructed to +elucidate the potential mechanisms of growth-promoting effects on rice growth +and P uptake in a series of pot experiments. Our results showed that the yield +and P uptake of intercropped rice were lower than those of rice grown in +monoculture. However, bacterial networks in the rice rhizosphere were more +stable in polyculture, exhibiting more hub nodes and greater modularity compared +to the rice monoculture. A bacterial synthetic community (SynCom) composed of +four bacterial strains (Variovorax paradoxus, Novosphingobium subterraneum, +Hydrogenophaga pseudoflava, Acidovorax sp.) significantly enhanced the biomass +and P uptake of potted rice plants. These growth-promoting effects are +underpinned by multiple pathways, including the direct activation of soil +available P, increased root surface area and root tip number, reduced root +diameter, and promotion of root-to-shoot P translocation through up-regulation +of Pi transporter genes (OsPht1;1, OsPht1;2, OsPht1;4, OsPht1;6). This study +highlights the potential of harnessing synthetic microbial communities to +enhance nutrient acquisition and improve crop production. + +DOI: 10.3390/ijms252312819 +PMCID: PMC11641191 +PMID: 39684532 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflicts of interest. \ No newline at end of file diff --git a/references_cache/pmid_39858916.txt b/references_cache/pmid_39858916.txt new file mode 100644 index 00000000..318a8c73 --- /dev/null +++ b/references_cache/pmid_39858916.txt @@ -0,0 +1,44 @@ +1. Microorganisms. 2025 Jan 13;13(1):148. doi: 10.3390/microorganisms13010148. + +Synthetic Microbial Communities Enhance Pepper Growth and Root Morphology by +Regulating Rhizosphere Microbial Communities. + +You T(1)(2)(3), Liu Q(2)(3), Chen M(1)(2)(3), Tang S(2), Ou L(1), Li D(2)(3). + +Author information: +(1)College of Horticulture, Hunan Agricultural University, Changsha 410125, +China. +(2)Hunan Provincial Key Laboratory of Agroecological Engineering, Key Laboratory +of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical +Agriculture, Chinese Academy of Sciences, Changsha 410125, China. +(3)Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang +Observation and Research Station for Karst Ecosystems, Chinese Academy of +Sciences, Huanjiang 547100, China. + +Synthetic microbial community (SynCom) application is efficient in promoting +crop yield and soil health. However, few studies have been conducted to enhance +pepper growth via modulating rhizosphere microbial communities by SynCom +application. This study aimed to investigate how SynCom inoculation at the +seedling stage impacts pepper growth by modulating the rhizosphere microbiome +using high-throughput sequencing technology. SynCom inoculation significantly +increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll +content, leaf number, root vigor, root tips, total root length, and +root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, +27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the +control. The Chao index of the rhizosphere microbial community and Bray-Curtis +dissimilarity of the fungal community significantly increased, while Bray-Curtis +dissimilarity of the bacterial community significantly decreased by SynCom +inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, +Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with +SynCom inoculation, and positively correlated with indices of pepper growth. Our +findings suggest that SynCom inoculation can effectively enhance pepper growth +and regulate root morphology by regulating rhizosphere microbial communities and +increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, +thereby benefiting nutrient acquisition, resistance improvement, and pathogen +resistance of crops to ensure sustainability. + +DOI: 10.3390/microorganisms13010148 +PMCID: PMC11767384 +PMID: 39858916 + +Conflict of interest statement: The authors declare no conflicts of interest. \ No newline at end of file diff --git a/references_cache/pmid_40020349.txt b/references_cache/pmid_40020349.txt new file mode 100644 index 00000000..79cdffce --- /dev/null +++ b/references_cache/pmid_40020349.txt @@ -0,0 +1,63 @@ +1. Water Res. 2025 Jun 1;277:123270. doi: 10.1016/j.watres.2025.123270. Epub 2025 + Feb 10. + +Synthetic microbial community maintains the functional stability of aerobic +denitrification under environmental disturbances: Insight into the mechanism of +interspecific division of labor. + +He Y(1), Yun H(2), Peng L(1), Wang W(1), Xu T(1), Zhang W(1), Li X(3). + +Author information: +(1)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou, 730000, China. +(2)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou, 730000, China; Gansu Key Laboratory of Biomonitoring and +Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou +University, Tianshui South Road #222, Lanzhou, 730000, China. Electronic +address: yunh@lzu.edu.cn. +(3)Ministry of Education Key Laboratory of Cell Activities and Stress +Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road +#222, Lanzhou, 730000, China; Gansu Key Laboratory of Biomonitoring and +Bioremediation for Environment Pollution, School of Life Sciences, Lanzhou +University, Tianshui South Road #222, Lanzhou, 730000, China. Electronic +address: xkli@lzu.edu.cn. + +Understanding how synthetic microbial community (SMC) respond to environmental +disturbances is the key to realizing SMC engineering applications. Here, dibutyl +phthalate (DBP) and levofloxacin (LOFX) were used as environmental disturbances +to study their effects on the aerobic denitrification functional stability of +SMC composed of Pseudomonas aeruginosa N2 (PA), Acinetobacter baumannii N1(AC) +and Aeromonas hydrophila (AH). The results showed that aerobic denitrification +efficiency could be maintained at about 93 % under DBP or LOFX disturbance, and +interspecific communication was mainly carried out through +N-butyryl-L-homoserine lactone (C4-HSL) and N-(3-oxododecanoyl)-L-homoserine +lactone (3OC12-HSL), correspondingly. DBP and LOFX induced the acceleration of +tricarboxylic acid (TCA) cycle, which facilitated the energy flux and +extracellular polymeric substances (EPS) production, thereby allowing SMC to +adapt to disturbances. Under DBP disturbance, DBP stimulated +phenazine-1-carboxylic acid production to accelerate electron transfer from the +quinone pool to complex III, resulting in an increase in electron transfer +activity. Up-regulation of complex I, complex III and heme synthesis genes under +LOFX disturbance led to enhanced denitrification enzymes expression and electron +transfer efficiency. SMC re-regulated different metabolic pathways to build +metabolic networks to maintain normal metabolic activity under different +disturbances. Overall, SMC maintained functional stability through the labor +division in modulation of interspecific communication, formation of defensive +barriers, promotion of energy flux, directional transfer of electron flux, and +reconstruction of metabolic networks. DBP stimulated AH and PA to occupy +functional dominance, while LOFX induced AC and PA to play a major role. The +understanding of the stability mechanism under different environmental +disturbances provides valuable guidance for stability maintenance and +engineering applications of SMC. + +Copyright © 2025. Published by Elsevier Ltd. + +DOI: 10.1016/j.watres.2025.123270 +PMID: 40020349 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_40266232.txt b/references_cache/pmid_40266232.txt new file mode 100644 index 00000000..67143b1b --- /dev/null +++ b/references_cache/pmid_40266232.txt @@ -0,0 +1,44 @@ +1. ISME J. 2025 Jan 2;19(1):wraf076. doi: 10.1093/ismejo/wraf076. + +Synthetic microbial community improves chicken intestinal homeostasis and +provokes anti-Salmonella immunity mediated by segmented filamentous bacteria. + +Zhang M(1), Shi S(1), Feng Y(1), Zhang F(1), Xiao Y(1), Li X(1), Pan X(2), Feng +Y(1), Liu D(1), Guo Y(1), Hu Y(1). + +Author information: +(1)State Key Laboratory of Animal Nutrition and Feeding, College of Animal +Science and Technology, China Agricultural University, Haidian District, Beijing +100193, China. +(2)Department of Microbiology, Beijing General Station of Animal Husbandry, +Chaoyang District, Beijing 100107, China. + +Applying synthetic microbial communities to manipulate the gut microbiota is a +promising manner for reshaping the chicken gut microbial community. However, it +remains elusive the role of a designed microbial community in chicken +physiological metabolism and immune responses. In this study, we constructed a +10-member synthetic microbial community (SynComBac10) that recapitulated the +phylogenetic diversity and functional capability of adult chicken intestinal +microbiota. We found that early-life SynComBac10 exposure significantly enhanced +chicken growth performance and facilitated the maturation of both the intestinal +epithelial barrier function and the gut microbiota. Additionally, SynComBac10 +promoted the pre-colonization and growth of segmented filamentous bacteria +(SFB), which in turn induced Th17 cell-mediated immune responses, thereby +conferring resistance to Salmonella infection. Through metagenomic sequencing, +we assembled the genomes of two distinct species of SFB from the chicken gut +microbiota, which displayed common metabolic deficiencies with SFB of other host +origins. In silico analyses indicated that the SynComBac10-stimulated early +establishment of SFB in the chicken intestine was likely through +SynComBac10-derived metabolite cross-feeding. Our study demonstrated the pivotal +role of a designed microbial consortium in promoting chicken gut homeostasis and +anti-infection immunity, providing a new avenue for engineering chicken gut +microbiota. + +© The Author(s) 2025. Published by Oxford University Press on behalf of the +International Society for Microbial Ecology. + +DOI: 10.1093/ismejo/wraf076 +PMCID: PMC12527353 +PMID: 40266232 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no competing interests. diff --git a/references_cache/pmid_40270813.txt b/references_cache/pmid_40270813.txt new file mode 100644 index 00000000..b8c1640e --- /dev/null +++ b/references_cache/pmid_40270813.txt @@ -0,0 +1,58 @@ +1. Front Microbiol. 2025 Apr 9;16:1534327. doi: 10.3389/fmicb.2025.1534327. +eCollection 2025. + +Teosinte-derived SynCom and precision biofertilization modulate the maize +microbiome, enhancing growth, yield, and soil functionality in a Mexican field. + +Hernández-García JA(1), Bernal JS(2), Antony-Babu S(3), Villa-Tanaca L(1), +Hernández-Rodríguez C(1), De-la-Vega-Camarillo E(1)(2)(3). + +Author information: +(1)Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de +Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico +Nacional, Ciudad de México, México. +(2)Department of Entomology, Texas A&M University, College Station, TX, United +States. +(3)Department of Plant Pathology and Microbiology, Texas A&M University, College +Station, TX, United States. + +Modern agriculture faces the challenge of optimizing fertilization practices +while maintaining soil resilience and microbial diversity, both critical for +sustainable crop production. We evaluated the effects of multiple fertilization +strategies on soil microbial communities and plant performance, comparing +conventional methods (urea-based and phosphorus fertilizers applied manually or +via drone-assisted precision delivery) with biofertilization using a synthetic +microbial consortium (SynCom) derived from teosinte-associated microbes. This +SynCom consisted of seven bacterial strains: Serratia nematodiphila EDR2, +Klebsiella variicola EChLG19, Bacillus thuringiensis EML22, Pantoea agglomerans +EMH25, Bacillus thuringiensis EBG39, Serratia marcescens EPLG52, and Bacillus +tropicus EPP72. High-throughput sequencing revealed significant shifts in +bacterial and fungal communities across treatments. Untreated soils showed +limited diversity, dominated by Enterobacteriaceae (>70%). Conventional +fertilization gradually reduced Enterobacteriaceae while increasing Pseudomonas +and Lysinibacillus populations. Drone-assisted conventional fertilization +notably enhanced Acinetobacter and Rhizobiales growth. Biofertilization +treatments produced the most pronounced shifts, reducing Enterobacteriaceae +below 50% while significantly increasing beneficial taxa like Bacillus, Pantoea, +and Serratia. Network analysis demonstrated that microbial interaction +complexity increased across treatments, with Bacillus emerging as a keystone +species. Drone-assisted biofertilization fostered particularly intricate +microbial networks, enhancing synergistic relationships involved in nutrient +cycling and biocontrol, though maintaining the stability of these complex +interactions requires careful monitoring. Our findings provide key insights into +how precision biofertilization with teosinte-derived microbial consortia can +sustainably reshape the maize microbiome, improving crop performance and soil +resilience. + +Copyright © 2025 Hernández-García, Bernal, Antony-Babu, Villa-Tanaca, +Hernández-Rodríguez and De-la-Vega-Camarillo. + +DOI: 10.3389/fmicb.2025.1534327 +PMCID: PMC12015678 +PMID: 40270813 + +Conflict of interest statement: The authors declare that the research was +conducted without any commercial or financial relationships that could be +construed as a potential conflict of interest. The author(s) declared that they +were an editorial board member of Frontiers, at the time of submission. This had +no impact on the peer review process and the final decision. \ No newline at end of file diff --git a/references_cache/pmid_40433987.txt b/references_cache/pmid_40433987.txt new file mode 100644 index 00000000..b4c39f9c --- /dev/null +++ b/references_cache/pmid_40433987.txt @@ -0,0 +1,41 @@ +2. Adv Sci (Weinh). 2025 Aug;12(31):e14232. doi: 10.1002/advs.202414232. Epub +2025 May 28. + +Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium +nucleatum-infected Colorectal Cancer via Ecological Control. + +Zhou Z(1), Yang M(1), Fang H(1), Zhang B(1), Ma Y(1), Li Y(1), Liu Y(1), Cheng +Z(1), Zhao Y(1), Si Z(1), Zhu H(1), Chen P(1). + +Author information: +(1)School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, +Gansu, 730000, P. R. China. + +Polymorphic microbiomes play important roles in colorectal cancer (CRC) +occurrence and development. In particular, Fusobacterium nucleatum (F. +nucleatum) is prevalent in patients with CRC, and eliminating it is beneficial +for treatment. Here, multiple metagenomic sequencing cohorts are combined with +multiomics to analyze the microbiome and related functional alterations. +Furthermore, local human metagenome and metabolomics are used to discover +commensal consortia. A synthetic microbial community (SynCom) is then designed +by metabolic network reconstruction, and its performance is validated using +coculture experiments and an AOM-DSS induced mouse CRC model. The sequencing +result shows that F. nucleatum is more abundant in both the feces and tumor +tissues of CRC patients. It causes alterations through various pathways, +including microbial dysbiosis, lipid metabolism, amino acid metabolism, and bile +acid metabolism disorders. The designed SynCom contains seven species with low +competition interrelationship. Furthermore, the SynCom successfully inhibits F. +nucleatum growth in vitro and achieves colonization in vivo. Additionally, it +promotes F. nucleatum decolonization, and enhances tryptophan metabolism and +secondary bile acid conversion, leading to reduced lipid accumulation, decreased +inflammatory reaction, and enhanced tumor inhibition effect. Overall, the +bottom-up designed SynCom is a controllable and promising approach for treating +F. nucleatum-positive CRC. + +© 2025 The Author(s). Advanced Science published by Wiley‐VCH GmbH. + +DOI: 10.1002/advs.202414232 +PMCID: PMC12376641 +PMID: 40433987 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflicts of interest. diff --git a/references_cache/pmid_40508300.txt b/references_cache/pmid_40508300.txt new file mode 100644 index 00000000..efb60aa5 --- /dev/null +++ b/references_cache/pmid_40508300.txt @@ -0,0 +1,44 @@ +1. Plants (Basel). 2025 May 26;14(11):1625. doi: 10.3390/plants14111625. + +Application of a Synthetic Microbial Community to Enhance Pepper Resistance +Against Phytophthora capsici. + +Bashizi TF(1), Kim MJ(2), Lim K(1), Lee G(1), Tagele SB(3), Shin JH(1). + +Author information: +(1)Department of Applied Biosciences, Kyungpook National University, Daegu +41566, Republic of Korea. +(2)NGS Core Facility, Kyungpook National University, Daegu 41566, Republic of +Korea. +(3)Department of Microbiology and Plant Pathology, University of California +Riverside, Riverside, CA 92507, USA. + +Pepper (Capsicum annuum) production faces significant challenges from soil-borne +pathogens, particularly Phytophthora capsici, which induces root rot and +damping-off diseases. Management of this pathogen remains challenging owing to +the scarcity of resistant cultivars and the ineffectiveness of chemical control +methods. A single strain has been used to prevent pathogenic disease, and this +approach limits the exploration of consortia comprising different genera. In +this study, we isolated five bacterial strains (Bacillus sp. T3, Flavobacterium +anhuiense T4, Cytobacillus firmus T8, Streptomyces roseicoloratus T14, and +Pseudomonas frederiksbergensis A6) from the rhizosphere of healthy pepper +plants. We then applied this 5-isolate synthetic microbial community (SynCom) to +Capsicum annuum to evaluate its efficacy in improving pepper resilience against +P. capsici. The SynCom members exhibited phosphate solubilization, +indole-3-acetic acid production, catalase activity, siderophore synthesis, and +strong antagonism against P. capsici. The SynCom reduced disease severity and +enhanced the growth of pepper plants. Furthermore, the beneficial genera such as +Bacillus, Fusicolla, and Trichoderma, significantly increased in the rhizosphere +of pepper after the application of the SynCom. Microbial functional prediction +analysis revealed that these microbial shifts were associated with nitrogen +cycling and pathogen suppression. Our SynCom approach demonstrates the +effectiveness of microbial consortia in promoting the growth of +pathogen-infected plants by reprogramming the microbial community in the +rhizosphere. + +DOI: 10.3390/plants14111625 +PMCID: PMC12157186 +PMID: 40508300 + +Conflict of interest statement: The authors have no conflict of interest to +declare. \ No newline at end of file diff --git a/references_cache/pmid_40536564.txt b/references_cache/pmid_40536564.txt new file mode 100644 index 00000000..623365a8 --- /dev/null +++ b/references_cache/pmid_40536564.txt @@ -0,0 +1,46 @@ +1. Appl Microbiol Biotechnol. 2025 Jun 19;109(1):149. doi: +10.1007/s00253-025-13522-1. + +Establishing a co-culture aggregate of N-cycle bacteria to elucidate +flocculation in biological wastewater treatment. + +Parret L(1), Simoens K(1), Horemans B(1)(2), De Vrieze J(3)(4), Smets I(5). + +Author information: +(1)Department of Chemical Engineering, Bio- & Chemical Reactor Engineering and +Safety (CREaS), KU Leuven, Celestijnenlaan 200F box 2424, B-3001, Leuven, +Belgium. +(2)Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, +B-3001, Leuven, Belgium. +(3)Centre for Microbial Ecology and Technology (CMET), Ghent University, Frieda +Saeysstraat 1, B-9052, Gent, Belgium. +(4)Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), +Frieda Saeysstraat 1, B-9052, Gent, Belgium. +(5)Department of Chemical Engineering, Bio- & Chemical Reactor Engineering and +Safety (CREaS), KU Leuven, Celestijnenlaan 200F box 2424, B-3001, Leuven, +Belgium. ilse.smets@kuleuven.be. + +Biological flocculation is a complex phenomenon that is often treated as a black +box. As a result, flocculation problems are usually remediated without knowledge +of the exact causes. We show that it is feasible to exploit a model (N-cycle) +consortium with reduced complexity to fundamentally study bioflocculation. +Strong nitrifier microcolonies were formed during oxic/anoxic cycles in +sequencing batch reactors, using alginate entrapment as a cell retention system. +After the release of these aggregates into suspension, macroclusters with flocs +of the denitrifier were observed. These results suggest that a living model of a +full-scale activated sludge floc can be built through the use of this bottom-up +approach. By eliminating shifts in the microbial community, the applied +experimental conditions have a more direct effect on the observations. Key +Points  ∙  Studying flocculation with a model consortium is feasible  ∙  +Alginate entrapment leads to strong microcolony formation of nitrifiers  ∙  FISH +by itself is not suitable to study aggregation of a coculture. + +© 2025. The Author(s). + +DOI: 10.1007/s00253-025-13522-1 +PMCID: PMC12178987 +PMID: 40536564 [Indexed for MEDLINE] + +Conflict of interest statement: Declarations. Conflict of interest: The authors +declare no competing interests. Ethical approval: This article does not contain +any studies with human participants or animals performed by any of the authors. \ No newline at end of file diff --git a/references_cache/pmid_40670700.txt b/references_cache/pmid_40670700.txt new file mode 100644 index 00000000..55b09334 --- /dev/null +++ b/references_cache/pmid_40670700.txt @@ -0,0 +1,56 @@ +1. Appl Microbiol Biotechnol. 2025 Jul 16;109(1):168. doi: +10.1007/s00253-025-13547-6. + +Development of a chemotactic SynCom bioorganic fertilizer for biocontrol of +bacterial wilt in tobacco fields. + +Liu Y(#)(1), Zhang W(#)(2), Guo L(2), Li H(1), Zhu J(1), Li X(3), Zhang X(2), +Yang X(2), Xu Y(2), Shen Q(2), Yang T(4), Wei Z(2). + +Author information: +(1)Guizhou Academy of Tobacco Science, Guiyang, 550081, China. +(2)Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of +Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center for +Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving +fertilizers, Nanjing Agricultural University, Nanjing, 210095, China. +(3)Guizhou Tobacco Corporation of CNTC, Guiyang, 550003, China. +newcool1361214@163.com. +(4)Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of +Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center for +Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving +fertilizers, Nanjing Agricultural University, Nanjing, 210095, China. +tjyang@njau.edu.cn. +(#)Contributed equally + +Bacterial wilt caused by Ralstonia solanacearum is one of the most severe plant +diseases all over the world. Currently, many scientists are using SynCom +(synthetic microbial community) to control this disease. However, designing of +highly efficient SynCom remains challenging. In this study, we isolated 372 +bacteria with different morphologies from the rhizosphere soil of healthy +tobacco plants in a diseased field. Based on the antagonistic activity, +compatibility, and presence of cheA gene, a marker gene of chemotaxis, we +constructed a chemotactic SynCom comprising two Pseudomonas strains and one +Bacillus strain. In vitro experiments revealed that vitamin C, propionic acid, +and esculetin significantly promoted the growth and antagonistic ability of +chemotactic SynCom strains. Next, we optimized the proportion of organic +fertilizer to support the growth of the SynCom strains. The application of the +bioorganic fertilizer containing chemotactic SynCom can protect diseased tobacco +field from R. solanacearum invasion and enhance yields. Finally, rhizosphere +bacterial community analysis showed that phyla Bacillota and Chloroflexiota were +significantly enriched. This study highlights the potential of chemotactic +SynCom for effective biocontrol, offering a new approach for managing bacterial +wilt and enhancing crop yields. KEY POINTS: • The bioorganic fertilizer +containing chemotactic SynCom suppresses R. solanacearum and boosts tobacco +yields. • Root exudate-selected prebiotics enhance the antagonistic effects of +SynCom against pathogens. • SynCom bioorganic fertilizer regulates the +rhizosphere microbiome, enriching beneficial bacterial phyla. + +© 2025. The Author(s). + +DOI: 10.1007/s00253-025-13547-6 +PMCID: PMC12267373 +PMID: 40670700 [Indexed for MEDLINE] + +Conflict of interest statement: Declarations. Ethical approval: This article +contains no studies with human participants or animals performed by any authors. +Competing interests: The authors declare no competing interests. \ No newline at end of file diff --git a/references_cache/pmid_40853002.txt b/references_cache/pmid_40853002.txt new file mode 100644 index 00000000..7d5e0b4c --- /dev/null +++ b/references_cache/pmid_40853002.txt @@ -0,0 +1,51 @@ +1. mSphere. 2025 Sep 30;10(9):e0015925. doi: 10.1128/msphere.00159-25. Epub 2025 +Aug 25. + +Synthetic communities of maize root bacteria interact and redirect benzoxazinoid +metabolization. + +Thoenen L(1)(2), Pestalozzi C(2), Zuest T(1)(3), Kreuzer M(4), Mateo P(1), +Karasawa M(2), Deslandes G(1), Robert CA(1), Bruggmann R(4), Erb M(1), Schlaeppi +K(1)(2). + +Author information: +(1)Institute of Plant Sciences, University of Bern, Bern, Switzerland. +(2)Department of Environmental Sciences, University of Basel, Basel, +Switzerland. +(3)Department of Systematic and Evolutionary Botany, University of Zurich, +Zurich, Switzerland. +(4)Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland. + +Plant roots are colonized by diverse microbial communities. These communities +are shaped by root exudates, including plant-specialized metabolites. +Benzoxazinoids are such secreted compounds of maize. Individual microbes differ +in their ability to tolerate and metabolize antimicrobial benzoxazinoids. To +investigate how these traits combine in a community, we designed two synthetic +communities of maize root bacteria that share six common strains and differ in +their ability to metabolize benzoxazinoids based on the seventh strain. We +exposed both communities to the benzoxazinoid MBOA +(6-methoxybenzoxazolin-2(3H)-one) in vitro and found that the metabolizing +community did not degrade MBOA to its aminophenoxazinone, as observed for +individual strains, but, as a community, they formed the corresponding +acetamide. MBOA shaped the differential compositions of both communities and +increased the fraction of MBOA-tolerant strains. The benzoxazinoid-metabolizing +community showed a higher tolerance to MBOA and was able to utilize MBOA as +their sole carbon source for growth. Hence, bacterial interaction results in +alternative benzoxazinoid metabolization and increases community performance in +the presence of these antimicrobial compounds. Future work is needed to uncover +the genetics of this metabolic interaction and ecological consequences for the +bacterial community and the host plant.IMPORTANCEWe investigated how maize root +bacteria-alone or in community-tolerate and metabolize antimicrobial compounds +of their host plant. We found that the capacity to metabolize such a compound +impacts bacterial community size and structure and, most importantly, benefits +community fitness. We also found that interacting bacteria redirected the +metabolization of the antimicrobial compound to an alternative degradation +pathway. Our work highlights the need to study the teamwork of microbes to +uncover their community traits to ultimately understand the ecological +consequences for the bacterial community and eventually the host plant. + +DOI: 10.1128/msphere.00159-25 +PMCID: PMC12483121 +PMID: 40853002 [Indexed for MEDLINE] + +Conflict of interest statement: The authors declare no conflict of interest. \ No newline at end of file diff --git a/references_cache/pmid_40862137.txt b/references_cache/pmid_40862137.txt new file mode 100644 index 00000000..9777f4e4 --- /dev/null +++ b/references_cache/pmid_40862137.txt @@ -0,0 +1,58 @@ +1. Front Microbiol. 2025 Aug 11;16:1649750. doi: 10.3389/fmicb.2025.1649750. +eCollection 2025. + +A stable 15-member bacterial SynCom promotes Brachypodium growth under drought +stress. + +Yadav A(#)(1), Chen M(#)(1), Acharya SM(1), Kim G(2), Yang Y(1), Zhao TZ(1), +Tsang E(1), Chakraborty R(1). + +Author information: +(1)Climate and Ecosystem Sciences Division, Earth & Environmental Sciences Area, +Lawrence Berkeley National Laboratory, Berkeley, CA, United States. +(2)Department of Molecular and Cell Biology, University of California Berkeley, +Berkeley, CA, United States. +(#)Contributed equally + +INTRODUCTION: Rhizosphere microbiomes are known to drive soil nutrient cycling +and influence plant fitness during adverse environmental conditions. +Field-derived robust Synthetic Communities (SynComs) of microbes mimicking the +diversity of rhizosphere microbiomes can greatly advance a deeper understanding +of such processes. However, assembling stable, genetically tractable, +reproducible, and scalable SynComs remains challenging. +METHODS: Here, we present a systematic approach using a combination of network +analysis and cultivation-guided methods to construct a 15-member SynCom from the +rhizobiome of Brachypodium distachyon. This SynCom incorporates diverse strains +from five bacterial phyla. Genomic analysis of the individual strains was +performed to reveal encoded plant growth-promoting traits, including genes for +the synthesis of osmoprotectants (trehalose and betaine) and Na+/K+ +transporters, and some predicted traits were validated by laboratory phenotypic +assays. +RESULTS: The SynCom demonstrates strong stability both in vitro and in planta. +Most strains encoded multiple plant growth-promoting functions, and several of +these were confirmed experimentally. The presence of osmoprotectant and ion +transporter genes likely contributed to the observed resilience of Brachypodium +to drought stress, where plants amended with the SynCom recovered better than +those without. We further observed preferential colonization of SynCom strains +around root tips under stress, likely due to active interactions between plant +root metabolites and bacteria. +DISCUSSION: Our results demonstrate that trait-informed construction of +synthetic communities can yield stable, functionally diverse consortia that +enhance plant resilience under drought. Preferential colonization near root tips +points to active, localized plant-microbe signaling as a component of +stress-responsive recruitment. This stable SynCom provides a scalable platform +for probing mechanisms of plant-microbe interaction and for developing +microbiome-based strategies to improve soil and crop performance in variable +environments. + +Copyright © 2025 Yadav, Chen, Acharya, Kim, Yang, Zhao, Tsang and Chakraborty. + +DOI: 10.3389/fmicb.2025.1649750 +PMCID: PMC12375656 +PMID: 40862137 + +Conflict of interest statement: The authors declare that the research was +conducted in the absence of any commercial or financial relationships that could +be construed as a potential conflict of interest. The author(s) declared that +they were an editorial board member of Frontiers, at the time of submission. +This had no impact on the peer review process and the final decision. \ No newline at end of file diff --git a/references_cache/pmid_41264879.txt b/references_cache/pmid_41264879.txt new file mode 100644 index 00000000..d2b9a424 --- /dev/null +++ b/references_cache/pmid_41264879.txt @@ -0,0 +1,32 @@ +1. Environ Sci Technol. 2025 Dec 9;59(48):25960-25972. doi: +10.1021/acs.est.5c07865. Epub 2025 Nov 20. + +Synthetic Microbial Community Promotes Straw Humification and Improves Soil +Organic Carbon in Cropland. + +Wang X(1), Wang L(1), Han X(1), Wang L(1), Zhang Y(1). + +Author information: +(1)School of Resources and Environment, Northeast Agricultural University, +Harbin 150030, China. + +Straw return is considered an effective approach to increase soil organic carbon +(SOC) and improve soil multifunctionality (SMF), yet the relatively low +humification rate under field conditions limits these benefits. The application +of synthetic microbial communities (SynComs) represents a promising strategy for +promoting straw humification. Nevertheless, challenges remain in designing +functionally stable SynComs for straw humification. Here, by combining +progressive dilution-microcosm cultivation with co-occurrence network and +functional analyses, we identified keystone taxa that promoted maize straw +humification in the microcosm. From these taxa, we constructed a two-membered +SynCom (Bacillus siamensis B and Bradyrhizobium japonicum G). By cross-feeding, +SynCom members enable each other to grow, increase the activities of key enzymes +(carboxymethyl cellulase, xylanase, lignin peroxidase, and nitrogenase), and +thereby promote maize straw humification. Field experiments further demonstrated +that SynCom inoculation enhanced the in vivo turnover pathway of the microbial +carbon pump, thereby promoting straw humification and improving SOC. Overall, we +provide a systematic approach for identifying and applying keystone taxa to +construct SynComs that promote maize straw humification and improve SOC. + +DOI: 10.1021/acs.est.5c07865 +PMID: 41264879 [Indexed for MEDLINE] \ No newline at end of file diff --git a/references_cache/pmid_41932525.txt b/references_cache/pmid_41932525.txt new file mode 100644 index 00000000..668c155b --- /dev/null +++ b/references_cache/pmid_41932525.txt @@ -0,0 +1,58 @@ +1. Bioresour Technol. 2026 Jul;451:134546. doi: 10.1016/j.biortech.2026.134546. +Epub 2026 Apr 1. + +Synthetic microbial community drive methane oxidation coupled to Cr(VI) +reduction via division of labor and extracellular electron transfer. + +Liu Q(1), Wei S(1), Li Y(2), Yu X(1), Zhang Z(1), Li J(3). + +Author information: +(1)College of Resources and Environmental Engineering, Key Laboratory of Karst +Georesources and Environment, Ministry of Education, Guizhou University, Guiyang +550025, China. +(2)College of Resources and Environmental Engineering, Key Laboratory of Karst +Georesources and Environment, Ministry of Education, Guizhou University, Guiyang +550025, China; Guizhou Karst Environmental Ecosystems Observation and Research +Station, Ministry of Education, Guiyang 550025, China; Guizhou Provincial Key +Laboratory for Prevention and Control of Emerging Contaminants, Guiyang 550025, +China. Electronic address: ycli3@gzu.edu.cn. +(3)College of Resources and Environmental Engineering, Key Laboratory of Karst +Georesources and Environment, Ministry of Education, Guizhou University, Guiyang +550025, China; Guizhou Karst Environmental Ecosystems Observation and Research +Station, Ministry of Education, Guiyang 550025, China; Guizhou Provincial Key +Laboratory for Prevention and Control of Emerging Contaminants, Guiyang 550025, +China. + +While methane oxidation coupled to Cr(VI) reduction has been widely +investigated, the functional specialization and division of labor within +microbial consortia remain insufficiently understood. In this study, a synthetic +microbial community (SynCom) was constructed by controlling methane +concentration and chromium load. The maximum Cr(VI) removal load of this system +reached 20.63 mg/L/d. The metagenomic assembly genome analysis showed that under +hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving +methane oxidation. It achieved extracellular electron transfer (EET) through +multiheme c-type cytochromes and conductive pili, or jointly with dominant +genera such as Hyphomicrobium and Thiobacillus, to couple methane oxidation with +Cr(VI) reduction. Integrated multi-omics revealed significant enrichment of +differentially expressed proteins involved in quorum sensing and methane +metabolism, along with elevated expression of ABC transporter substrate-binding +protein and porin. The primary metabolites included N-Methyl-L-Proline, +L-Histidine, and Hypaphorin, with L-Glutamine serving as a central node +connecting the highest number of pathways in the metabolic network. The +inhibition experiments confirmed that inhibiting the methane oxidation would +directly reduce the efficiency of Cr(VI) reduction. This study revealed the +microbial division of labor and the microscopic process of EET driven by aerobic +methanotrophs under hypoxic conditions, and expanded its application potential +in bioremediation from the perspective of SynCom. It could be a scientific +foundation for pollution control technologies of methane-based biotransformation +and utilization. + +Copyright © 2026. Published by Elsevier Ltd. + +DOI: 10.1016/j.biortech.2026.134546 +PMID: 41932525 [Indexed for MEDLINE] + +Conflict of interest statement: Declaration of competing interest The authors +declare that they have no known competing financial interests or personal +relationships that could have appeared to influence the work reported in this +paper. \ No newline at end of file diff --git a/references_cache/pmid_42007760.txt b/references_cache/pmid_42007760.txt new file mode 100644 index 00000000..53324958 --- /dev/null +++ b/references_cache/pmid_42007760.txt @@ -0,0 +1,58 @@ +3. Appl Environ Microbiol. 2026 Apr 20:e0254825. doi: 10.1128/aem.02548-25. +Online ahead of print. + +A synthetic microbial community for soybean biofertilization designed via +chlorophyll-based iterative selection. + +Brignoli D(1)(2), Colla D(1), Frickel-Critto E(3), Castells CB(3), Pérez-Giménez +J(1), Lodeiro AR(1)(2). + +Author information: +(1)Instituto de Biotecnología y Biología Molecular (IBBM)-Facultad de Ciencias +Exactas, Universidad Nacional de La Plata (UNLP) y CCT-La Plata, CONICET, La +Plata, Argentina. +(2)Cátedra de Genética-Facultad de Ciencias Agrarias y Forestales, Universidad +Nacional de La Plata (UNLP), La Plata, Argentina. +(3)Laboratorio de Investigación y Desarrollo de Métodos Analíticos, Universidad +Nacional de La Plata (UNLP) y CIC-PBA, La Plata, Argentina. + +Improving the effectiveness of microbial inoculants for soybean is essential to +enhance biological nitrogen fixation and reduce fertilizer dependence; however, +inoculated Bradyrhizobium strains frequently display inconsistent field +performance. Inoculation is usually carried out with single-strain formulations, +overlooking the possible influence of the native soil microbiota on nodulation +success. This limitation may be addressed by formulating inoculants with +consortia that include selected members of the soil microbiota. To this end, a +synthetic microbial community (SynCom) was developed through a host-mediated +microbiome engineering approach guided by leaf chlorophyll content as a rapid, +non-destructive plant trait. The experiment was initiated by inoculating soybean +plants with a consortium of 9 Bradyrhizobium spp. and 14 non-rhizobial soil +isolates. Across eight consecutive selection rounds under gnotobiotic +conditions, rhizosphere communities associated with superior plant performance +were pooled and propagated. Recurrent selection induced significant shifts in +community composition, consistently favoring Bradyrhizobium diazoefficiens as +the dominant nodulating member and enriching taxa from Pseudomonadales, +Burkholderiales, and Sphingomonadales. Sequencing-based profiling and network +analysis suggested the emergence of a cohesive and functionally enriched +community, with increased potential for nitrogen transformations and organic +matter turnover. When evaluated in non-sterile soil, the SynCom derived from the +sixth selection round increased nodule number and biomass relative to an +uninoculated control and a commercial inoculant strain. These results suggest +that plant-guided selection can steer rhizosphere community assembly toward +beneficial configurations and support the development of improved soybean +bioinoculants.IMPORTANCESoybean [Glycine max (L.) Merr.] is a major global crop +characterized by high seed protein content, which demands elevated nitrogen +assimilation. To meet this demand, the crop can utilize atmospheric nitrogen +through the process of biological nitrogen fixation in symbiosis with +Bradyrhizobium bacteria, thus mitigating soil nitrogen depletion. Although +Bradyrhizobium-based inoculants are applied at sowing, their interplay with +other members of the rhizosphere microbiota remains poorly understood. It is +well documented that plants and rhizosphere microbiota interact to shape plant +growth and soil productivity. Therefore, this work evaluated the inoculation of +soybean with a synthetic microbial consortium as a strategy to develop +new-generation inoculants. These bioinputs are designed to harness +plant-soil-microbe interactions to improve soybean productivity while preserving +soil properties. + +DOI: 10.1128/aem.02548-25 +PMID: 42007760