diff --git a/kb/communities/DVM_Triculture.yaml b/kb/communities/DVM_Triculture.yaml index 3fbb7184..059ec560 100644 --- a/kb/communities/DVM_Triculture.yaml +++ b/kb/communities/DVM_Triculture.yaml @@ -375,6 +375,62 @@ environmental_factors: snippet: We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate explanation: Quantifies enhanced productivity from tri-culture interactions +related_ingredients: +- preferred_term: lactate + chebi_term: + id: CHEBI:24996 + label: lactate + relevance: Primary carbon and energy source for the tri-culture; oxidized by D. vulgaris to + acetate, CO2, and H2, initiating the syntrophic chain that drives methanogenesis. + evidence: + - reference: PMID:16345708 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: degraded lactate, with the production of acetate and CH(4) + explanation: Names lactate as the substrate whose syntrophic degradation feeds the community, + anchoring it as the central input compound. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Central intermediate produced by D. vulgaris lactate oxidation and consumed by + M. barkeri for acetotrophic methanogenesis; its accumulation and utilization shape the + sulfate-dependent community response. + evidence: + - reference: PMID:16345708 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: lactate, with the production of acetate and CH(4) + explanation: Identifies acetate as a direct product of lactate degradation, anchoring it + as a key syntrophic intermediate. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Terminal product of the tri-culture; combined hydrogenotrophic and acetotrophic + methanogenesis nearly doubles methane yield relative to co-cultures in the absence of sulfate. + evidence: + - reference: doi:10.1098/rsif.2019.0129 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: increase methane production by almost twofold compared to co-cultures and are stable + in the absence of sulfate + explanation: Anchors methane as the quantified terminal output of the community and the + metric of its productivity. +- preferred_term: sulfate + chebi_term: + id: CHEBI:16189 + label: sulfate + relevance: Geochemical regulator of the community; serves as an alternative electron acceptor + for D. vulgaris, shifting it from syntrophic growth to sulfate reduction and altering + methanogen competition. + evidence: + - reference: doi:10.1098/rsif.2019.0129 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: their stability against sulfate availability are not well understood + explanation: Anchors sulfate availability as the central environmental variable controlling + community stability and productivity. metals_present: [] metal_relevance: SIGNIFICANT metal_notes: Metal/REE detected via environmental factor measurements diff --git a/kb/communities/Geobacter_Clostridium_DIET.yaml b/kb/communities/Geobacter_Clostridium_DIET.yaml index ccd6ddae..43dc635d 100644 --- a/kb/communities/Geobacter_Clostridium_DIET.yaml +++ b/kb/communities/Geobacter_Clostridium_DIET.yaml @@ -437,6 +437,48 @@ growth_media: explanation: Establishes anaerobic requirement maintained using Hungate technique culturemech_id: CultureMech:015432 culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:015432 +related_ingredients: +- preferred_term: glycerol + chebi_term: + id: CHEBI:17754 + label: glycerol + relevance: Central fermentable substrate of the coculture; C. pasteurianum ferments + glycerol and DIET from G. sulfurreducens redirects its fermentation product profile. + evidence: + - reference: PMID:28287150 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The present study deals with a co-culture of Geobacter sulfurreducens and + Clostridium pasteurianum during glycerol fermentation + explanation: Identifies glycerol as the fermentation substrate of the coculture. +- preferred_term: 1,3-propanediol + chebi_term: + id: CHEBI:16109 + label: propane-1,3-diol + relevance: Key DIET-enhanced product; electron transfer shifts C. pasteurianum carbon + flux toward increased 1,3-propanediol, the industrially relevant target metabolite. + evidence: + - reference: PMID:28287150 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: pasteurianum metabolic pattern was significantly altered towards improved + 1,3-propanediol and butyrate production (+37% and +38% resp.) + explanation: Anchors 1,3-propanediol as the metabolite increased by DIET-induced + metabolic shift. +- preferred_term: butyrate + chebi_term: + id: CHEBI:17968 + label: butyrate + relevance: Co-enhanced DIET product; alongside 1,3-propanediol, butyrate production + rises (+38%) when C. pasteurianum receives electrons from G. sulfurreducens. + evidence: + - reference: PMID:28287150 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: pasteurianum metabolic pattern was significantly altered towards improved + 1,3-propanediol and butyrate production (+37% and +38% resp.) + explanation: Anchors butyrate as a metabolite increased by the DIET-induced metabolic + shift. metals_present: [] metal_relevance: SIGNIFICANT metal_notes: Metal/REE detected via environmental factor measurements diff --git a/kb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml b/kb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml index 03a3c5cd..d0230208 100644 --- a/kb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml +++ b/kb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml @@ -310,6 +310,35 @@ external_resources: evidence_source: IN_VITRO snippet: Geobacter sulfurreducens in Coculture with Pseudomonas aeruginosa explanation: Supports this source as an exact species-composition coculture publication. +related_ingredients: +- preferred_term: formate + chebi_term: + id: CHEBI:15740 + label: formate + relevance: Central electron donor preferentially utilized by P. aeruginosa in + the restricted medium, making it one of the two complementary substrates that + force cooperative coculture metabolism. + evidence: + - reference: PMID:28992596 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: preferential utilization of formate and fumarate by P. aeruginosa and G. + explanation: Snippet names formate explicitly as the substrate preferentially + utilized by P. aeruginosa in the coculture medium. +- preferred_term: fumarate + chebi_term: + id: CHEBI:29806 + label: fumarate(2-) + relevance: Central electron acceptor preferentially utilized by G. sulfurreducens + in the restricted medium, complementing formate to drive syntrophic coculture + growth that pure cultures cannot achieve. + evidence: + - reference: PMID:28992596 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: preferential utilization of formate and fumarate by P. aeruginosa and G. + explanation: Snippet names fumarate explicitly as the substrate preferentially + utilized by G. sulfurreducens in the coculture medium. metals_present: [] rare_earth_elements_present: [] metal_relevance: SIGNIFICANT diff --git a/kb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml b/kb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml index f4d78676..f0c6c630 100644 --- a/kb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml +++ b/kb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml @@ -222,6 +222,55 @@ growth_media: evidence_source: IN_VITRO snippet: For an N. frontalis-M. smithii coculture, the positive stimulation was maintained during an extended (18-day) incubation period explanation: Supports the extended N. frontalis-M. smithii coculture observation. +related_ingredients: +- preferred_term: xylan + chebi_term: + id: CHEBI:37166 + label: xylan + relevance: Xylan is the central polysaccharide substrate degraded by Neocallimastix frontalis, + driving the syntrophic fermentation and the entire coculture phenotype. + evidence: + - reference: PMID:16348244 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: in coculture with Methanobrevibacter smithii on xylan + explanation: Anchors xylan as the growth substrate for the fungus-methanogen coculture. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Hydrogen produced by fungal fermentation is consumed by the hydrogenotrophic methanogen, + making interspecies hydrogen transfer the core mechanistic coupling of the coculture. + evidence: + - reference: PMID:16348244 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: metabolite profiles became acetogenic as a result of interspecies hydrogen transfer + explanation: Anchors hydrogen as the transferred reducing equivalent driving the acetogenic shift. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Acetate accumulation increases as the fungal metabolite profile shifts toward acetogenesis + when hydrogen is removed by the methanogenic partner. + evidence: + - reference: PMID:16348244 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: more acetate and less lactate were formed, while formate and hydrogen did not accumulate + explanation: Anchors acetate as the favored fermentation product in the syntrophic coculture. +- preferred_term: formate + chebi_term: + id: CHEBI:15740 + label: formate + relevance: Formate is a fungal fermentation intermediate whose accumulation is prevented in coculture, + consistent with interspecies transfer of reducing equivalents to the methanogen. + evidence: + - reference: PMID:16348244 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: more acetate and less lactate were formed, while formate and hydrogen did not accumulate + explanation: Anchors formate as a fermentation intermediate that does not accumulate under syntrophy. associated_datasets: - name: Ruminal fungus-methanogen xylanolytic activity phenotypes dataset_type: PHENOTYPE diff --git a/kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml b/kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml index 4495ead1..240876a6 100644 --- a/kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml +++ b/kb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml @@ -345,6 +345,44 @@ external_resources: snippet: inter-species metabolite and electron transfer in a model microbial community explanation: Lists a computational publication about metabolite and electron transfer modeling in a model microbial community; the source article was checked for the exact composition. +related_ingredients: +- preferred_term: cellobiose + chebi_term: + id: CHEBI:17057 + label: cellobiose + relevance: Cellobiose is the shared carbon and energy input fermented by C. cellulolyticum, + whose products feed D. vulgaris and G. sulfurreducens; it is the central substrate of the + trophic model. + evidence: + - reference: doi:10.1186/1471-2180-10-149 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Cellobiose served as the carbon and energy source for C. cellulolyticum + explanation: Names cellobiose as the carbon and energy source fermented by C. cellulolyticum. +- preferred_term: sulfate + chebi_term: + id: CHEBI:16189 + label: sulfate + relevance: Sulfate is the electron acceptor supplied for D. vulgaris, defining its respiratory + niche within the three-species community. + evidence: + - reference: doi:10.1186/1471-2180-10-149 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: provided with sulfate and fumarate respectively as electron acceptors + explanation: Names sulfate as the supplied electron acceptor for D. vulgaris. +- preferred_term: fumarate + chebi_term: + id: CHEBI:29806 + label: fumarate(2-) + relevance: Fumarate is the electron acceptor supplied for G. sulfurreducens, defining its + respiratory niche within the three-species community. + evidence: + - reference: doi:10.1186/1471-2180-10-149 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: provided with sulfate and fumarate respectively as electron acceptors + explanation: Names fumarate as the supplied electron acceptor for G. sulfurreducens. associated_datasets: [] metals_present: [] rare_earth_elements_present: [] diff --git a/kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml b/kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml index 9d2d18cc..3ec796d6 100644 --- a/kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml +++ b/kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml @@ -332,6 +332,55 @@ external_resources: resource_id: NCBITaxon:2203 url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2203 description: NCBI Taxonomy record for Methanospirillum hungatei. +related_ingredients: +- preferred_term: benzoate + chebi_term: + id: CHEBI:16150 + label: benzoate + relevance: Aromatic growth substrate degraded by Syntrophus gentianae in the + syntrophic coculture; the central electron donor of the system. + evidence: + - reference: PMID:33657722 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: degraded benzoate to CH4 and acetate + explanation: Names benzoate as the substrate consumed by the coculture, anchoring it as the central degraded compound. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Interspecies electron carrier transferred from S. gentianae to M. + hungatei; its accumulation thermodynamically inhibits benzoate degradation. + evidence: + - reference: PMID:33657722 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Addition of a H2-oxidizing sulfate + explanation: References H2 (dihydrogen) as the interspecies intermediate whose oxidation drives benzoate degradation. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Major fermentation product of benzoate degradation whose + accumulation thermodynamically inhibits the fermenting bacterium. + evidence: + - reference: PMID:33657722 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: degraded benzoate to CH4 and acetate + explanation: Names acetate as a direct product of coculture benzoate degradation, anchoring it as a central intermediate. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Terminal methanogenic product formed by M. hungatei from the + interspecies reducing equivalents, defining the community output. + evidence: + - reference: PMID:33657722 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: degraded benzoate to CH4 and acetate + explanation: Names CH4 (methane) as the terminal product of methanogenic benzoate degradation in the coculture. metals_present: [] rare_earth_elements_present: [] metal_relevance: NOT_APPLICABLE diff --git a/kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml b/kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml index 252afd17..3bade72e 100644 --- a/kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml +++ b/kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml @@ -394,6 +394,59 @@ external_resources: evidence_source: IN_VITRO snippet: syntrophic acetate-oxidizing bacterium explanation: Links the type-strain publication for the bacterial member and syntrophic phenotype. +related_ingredients: +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Acetate is the central substrate oxidized by T. phaeum in this syntrophic + coculture, driving acetate-coupled methanogenesis. + evidence: + - reference: PMID:15866934 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: oxidized acetate rapidly and produced acetate + explanation: Anchors acetate as the substrate oxidized by the mixed T. phaeum and + M. thermautotrophicus system. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Hydrogen is the interspecies electron-carrier produced by T. phaeum during + acetate oxidation and consumed by the hydrogenotrophic methanogen. + evidence: + - reference: PMID:11872465 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: acetate-oxidizing hydrogen-producing bacterium + explanation: Anchors dihydrogen as the product of the acetate-oxidizing bacterium + transferred to the methanogenic partner. +- preferred_term: formate + chebi_term: + id: CHEBI:15740 + label: formate + relevance: Formate is the reduced product of the reversed electron transport mechanism + in T. phaeum, an alternative interspecies electron carrier to hydrogen. + evidence: + - reference: PMID:31849917 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: yielding formate as reduced product + explanation: Anchors formate as the reduced product of the acetate-oxidation mechanism + transferred to the methanogenic partner. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Methane is the terminal product of acetate conversion via hydrogenotrophic + methanogenesis by M. thermautotrophicus in this coculture. + evidence: + - reference: PMID:31849917 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: acetate conversion to CO2 and CH4 + explanation: Anchors methane (CH4) as the terminal product of syntrophic acetate + conversion. metals_present: [] rare_earth_elements_present: [] metal_relevance: NOT_APPLICABLE diff --git a/kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml b/kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml index 6ad5d69e..d54e5c7b 100644 --- a/kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml +++ b/kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml @@ -321,6 +321,58 @@ external_resources: evidence_source: IN_VITRO snippet: The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii explanation: Lists this publication as a second exact-composition source for the same species pair. +related_ingredients: +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Central syntrophic intermediate; hydrogen produced by fermentative T. + maritima is transferred to and consumed by the hydrogenotrophic methanogen, + relieving H2 product inhibition and boosting bacterial cell densities. + evidence: + - reference: PMID:16391122 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Interspecies H2 transfer resulted in three- to fivefold-higher T. maritima + cell densities + explanation: Names interspecies H2 (dihydrogen) transfer as the intermediate driving + the coculture growth response. + - reference: PMID:18636642 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Interactions involving hydrogen transfer were studied in a coculture of + two hyperthermophilic microorganisms + explanation: Anchors hydrogen as the transferred substrate central to the studied + coculture interaction. +- preferred_term: carbon dioxide + chebi_term: + id: CHEBI:16526 + label: carbon dioxide + relevance: Co-substrate for hydrogenotrophic methanogenesis; the methanogen grew + without externally supplied CO2, indicating CO2 from T. maritima fermentation + supports methanogenic growth in the coculture. + evidence: + - reference: PMID:18636642 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the methanogen was able to grow in the absence of externally supplied H(2) + and CO(2) + explanation: Names CO(2) (carbon dioxide) as a methanogenic substrate supplied + internally by the partner rather than externally. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Terminal product of the coculture; hydrogenotrophic methanogenesis + converts transferred H2 and CO2 to methane, the metabolic endpoint linking the + syntrophy to biogeochemical methane formation. + evidence: + - reference: PMID:18636642 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: increases in methanogenesis rates with temperature + explanation: Methanogenesis is the methane-forming process whose rate rises with + temperature, anchoring methane as the central product of the coculture. metals_present: [] rare_earth_elements_present: [] metal_relevance: NOT_APPLICABLE diff --git a/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml b/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml index 695c81ed..dca25595 100644 --- a/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml +++ b/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml @@ -337,6 +337,63 @@ external_resources: resource_id: NCBITaxon:2203 url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2203 description: NCBI Taxonomy record for Methanospirillum hungatei. +related_ingredients: +- preferred_term: butyrate + chebi_term: + id: CHEBI:17968 + label: butyrate + relevance: > + Butyrate is the central growth substrate of this triculture; S. wolfei + syntrophically oxidizes butyrate, and ES5 addition increased the rate of + butyrate consumption. + evidence: + - reference: PMID:35699440 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: rates of butyrate consumption + explanation: Anchors butyrate as the oxidized substrate whose consumption rate increased. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: > + Methane is the terminal product generated by M. hungatei from interspecies + electron carriers; volumetric methane production was the key performance + output that increased after ES5 addition. + evidence: + - reference: PMID:35699440 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: volumetric methane production + explanation: Anchors methane as the terminal methanogenic product measured in the coculture. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: > + Hydrogen is an interspecies electron carrier transferred from the + butyrate-oxidizing bacterium to the hydrogen-scavenging methanogen + M. hungatei, enabling thermodynamically favorable syntrophy. + evidence: + - reference: PMID:35699440 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: hydrogen/formate-scavenging methanogenic archaea + explanation: Anchors hydrogen as a scavenged interspecies electron carrier consumed by the methanogen. +- preferred_term: formate + chebi_term: + id: CHEBI:15740 + label: formate + relevance: > + Formate is the second interspecies electron carrier scavenged by the + methanogenic partner M. hungatei, providing the reducing equivalents that + couple butyrate oxidation to methanogenesis. + evidence: + - reference: PMID:35699440 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: hydrogen/formate-scavenging methanogenic archaea + explanation: Anchors formate as a scavenged interspecies electron carrier consumed by the methanogen. metals_present: [] rare_earth_elements_present: [] metal_relevance: NOT_APPLICABLE