diff --git a/kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml b/kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml index 3333ddd0..19518b5e 100644 --- a/kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml +++ b/kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml @@ -237,6 +237,37 @@ environmental_factors: energy generation pathways and imply that to understand microbial processes that sustain nutrient cycling, lifestyles not captured in pure culture must be considered. explanation: Quantifies growth conditions for the syntrophic consortium +related_ingredients: +- preferred_term: lactate + chebi_term: + id: CHEBI:24996 + label: lactate + relevance: Central carbon and electron-donor substrate of the syntrophy; D. vulgaris oxidizes + lactate to acetate, H2, and CO2 in the absence of sulfate, and lactate transport/oxidation genes + are upregulated during syntrophic growth. + evidence: + - reference: PMID:19581361 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: During syntrophic growth on lactate with a hydrogenotrophic methanogen, numerous genes involved + in electron transfer and energy generation were upregulated in D + explanation: Names lactate as the substrate consumed during syntrophic growth, anchoring it as the + central substrate compound of the consortium. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Key interspecies electron-carrier intermediate; H2 produced by D. vulgaris lactate oxidation + is consumed by the hydrogenotrophic methanogen, and low H2 partial pressure makes the otherwise + thermodynamically unfavorable oxidation feasible. + evidence: + - reference: PMID:19581361 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes + the decomposition of organic matter in most anoxic environments + explanation: Identifies hydrogen as the transferred intermediate between producer and consumer, + anchoring dihydrogen as the central interspecies electron carrier. metals_present: - IRON metal_relevance: SIGNIFICANT diff --git a/kb/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.yaml b/kb/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.yaml index bfca537a..d03e3d52 100644 --- a/kb/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.yaml +++ b/kb/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.yaml @@ -192,6 +192,55 @@ growth_media: evidence_source: IN_VITRO snippet: rumen fluid-vitamin-based medium explanation: Supports the medium used for Methanosarcina methanogenic activity. +related_ingredients: +- preferred_term: lactate + chebi_term: + id: CHEBI:24996 + label: lactate + relevance: Primary substrate added to the sulfate-free coculture; its degradation by D. desulfuricans + drives the entire syntrophic system, fueling methanogenesis by M. barkeri. + 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 degraded substrate yielding acetate and methane in the coculture. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Central intermediate produced during early lactate degradation and later consumed by + M. barkeri for acetoclastic methanogenesis, linking lactate oxidation to methane formation. + evidence: + - reference: PMID:16345708 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: stoichiometric production of acetate and CH(4) + explanation: Anchors acetate as a stoichiometric product of lactate degradation in the coculture. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Interspecies electron carrier produced by Desulfovibrio during lactate growth; its + accumulation regulates carbon flow by inhibiting acetate degradation by M. barkeri. + evidence: + - reference: PMID:16345708 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: H(2) produced by the Desulfovibrio species during + explanation: Anchors hydrogen (H2) as a Desulfovibrio-derived intermediate central to the syntrophy. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Terminal product of the coupled syntrophy, formed by M. barkeri from both the + H2-CO2 and acetate methanogenic routes. + evidence: + - reference: PMID:16345708 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Later, acetate was degraded to CH(4) and presumably to CO(2) + explanation: Anchors methane (CH4) as the terminal product formed by M. barkeri from acetate. associated_datasets: - name: Desulfovibrio-Methanosarcina lactate syntrophy publication dataset_type: PHENOTYPE diff --git a/kb/communities/Geobacter_Methanosaeta_DIET.yaml b/kb/communities/Geobacter_Methanosaeta_DIET.yaml index 7d161249..d45d5805 100644 --- a/kb/communities/Geobacter_Methanosaeta_DIET.yaml +++ b/kb/communities/Geobacter_Methanosaeta_DIET.yaml @@ -293,6 +293,47 @@ growth_media: specialized medium culturemech_id: CultureMech:015435 culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:015435 +related_ingredients: +- preferred_term: ethanol + chebi_term: + id: CHEBI:16236 + label: ethanol + relevance: Central electron-donor substrate oxidized by G. metallireducens to drive + DIET; stoichiometrically converted to methane in the coculture. + evidence: + - reference: doi:10.1039/C3EE42189A + supports: SUPPORT + evidence_source: IN_VITRO + snippet: defined co-cultures of Geobacter metallireducens and Methanosaeta harundinacea + which stoichiometrically converted ethanol to methane + explanation: Names ethanol as the substrate consumed by the DIET coculture, anchoring + it as the central electron-donor compound. +- preferred_term: carbon dioxide + chebi_term: + id: CHEBI:16526 + label: carbon dioxide + relevance: Terminal electron acceptor reduced to methane by M. harundinacea using + electrons received directly from G. metallireducens via DIET. + evidence: + - reference: doi:10.1039/C3EE42189A + supports: SUPPORT + evidence_source: IN_VITRO + snippet: M. harundinacea accepted electrons via DIET for the reduction of carbon + dioxide to methane + explanation: Anchors carbon dioxide as the compound reduced to methane during DIET-driven + methanogenesis. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Terminal product of the DIET coculture, formed by CO2 reduction in M. + harundinacea and representing stoichiometric conversion of the ethanol substrate. + evidence: + - reference: doi:10.1039/C3EE42189A + supports: SUPPORT + evidence_source: IN_VITRO + snippet: stoichiometrically converted ethanol to methane + explanation: Anchors methane as the end product of the coculture's electron flow. metals_present: [] metal_relevance: SIGNIFICANT metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected diff --git a/kb/communities/Geobacter_Methanosarcina_DIET.yaml b/kb/communities/Geobacter_Methanosarcina_DIET.yaml index a1a66e9a..193a161d 100644 --- a/kb/communities/Geobacter_Methanosarcina_DIET.yaml +++ b/kb/communities/Geobacter_Methanosarcina_DIET.yaml @@ -336,6 +336,61 @@ growth_media: explanation: Confirms ethanol as electron donor and DIET mechanism in coculture culturemech_id: CultureMech:015434 culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:015434 +related_ingredients: +- preferred_term: ethanol + chebi_term: + id: CHEBI:16236 + label: ethanol + relevance: Sole electron-donor substrate of the coculture; oxidized by G. metallireducens, + with the electrons transferred via DIET to drive methanogenesis. + evidence: + - reference: PMID:24837373 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: shared electrons via DIET during the stoichiometric conversion of ethanol + to methane + explanation: Names ethanol as the substrate stoichiometrically converted via DIET, + anchoring it as the central electron-donating compound. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Intermediate of ethanol oxidation; its metabolism distinguishes DIET-based + syntrophy from H2-mediated transfer in M. barkeri cocultures. + evidence: + - reference: PMID:24837373 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: metabolized little of the acetate that P.carbinolicus produced + explanation: Explicitly names acetate as a metabolic intermediate handled by M. + barkeri, anchoring the compound in the consortium's metabolism. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Terminal product of the consortium; M. barkeri reduces CO2 to methane + using DIET-derived electrons. + evidence: + - reference: PMID:24837373 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: shared electrons via DIET during the stoichiometric conversion of ethanol + to methane + explanation: Names methane as the stoichiometric end product of the DIET coculture, + anchoring it as the central output compound. +- preferred_term: carbon dioxide + chebi_term: + id: CHEBI:16526 + label: carbon dioxide + relevance: Terminal electron acceptor reduced to methane by M. barkeri using electrons + received via DIET. + evidence: + - reference: PMID:24837373 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: using either H2 or electrons derived from DIET for CO2 reduction + explanation: States that DIET-derived electrons drive CO2 reduction, anchoring + carbon dioxide as the electron-accepting substrate for methanogenesis. metals_present: [] metal_relevance: SIGNIFICANT metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected diff --git a/kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml b/kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml index 632bf754..02acfb52 100644 --- a/kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml +++ b/kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml @@ -342,6 +342,60 @@ external_resources: resource_id: NCBITaxon:1175444 url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1175444 description: NCBI Taxonomy record for Methanocella conradii. +related_ingredients: +- preferred_term: propionate + chebi_term: + id: CHEBI:17272 + label: propionate + relevance: > + Propionate is the central catabolic substrate oxidized by + P. thermopropionicum, defining the syntrophic propionate-oxidizing + methanogenic system. + evidence: + - reference: PMID:30038609 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: propionate-oxidizing + explanation: Anchors propionate as the substrate oxidized by the bacterial syntroph. +- preferred_term: formate + chebi_term: + id: CHEBI:15740 + label: formate + relevance: > + Formate is produced and consumed across the partners as an interspecies + electron carrier supporting syntrophic electron transfer. + evidence: + - reference: PMID:30038609 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: employing formate as an alternate electron carrier + explanation: Anchors formate as an interspecies electron carrier in the coculture. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: > + Hydrogen (H2/CO2) is an interspecies electron-transfer intermediate + feeding the hydrogenotrophic methanogenic partner. + evidence: + - reference: PMID:30038609 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: but not H2/CO2 + explanation: Anchors H2/CO2 as an interspecies transfer intermediate tested during syntrophy. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: > + Methane is the terminal product of hydrogenotrophic methanogenesis by + M. conradii in this coculture. + evidence: + - reference: PMID:30038609 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: methanogenesis in M. conradii + explanation: Anchors methane as the product of methanogenesis by the methanogenic partner. metals_present: [] rare_earth_elements_present: [] metal_relevance: NOT_APPLICABLE diff --git a/kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml b/kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml index 039e3b11..d4959d18 100644 --- a/kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml +++ b/kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml @@ -252,6 +252,27 @@ environmental_factors: was characterized explanation: Establishes syntrophic nature of the organism requiring close association with methanogenic partner +related_ingredients: +- preferred_term: propionate + chebi_term: + id: CHEBI:17272 + label: propionate + relevance: Propionate is the defining growth substrate of this syntrophy. Pelotomaculum + thermopropionicum oxidizes propionate to acetate, CO2, and H2, but only in coculture + with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus, which + removes H2 and keeps the reaction thermodynamically feasible. Propionate is therefore + the central electron/carbon input that the entire two-member consortium is organized + around. + evidence: + - reference: PMID:12361280 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The strain grew on propionate, ethanol, lactate, 1-butanol, 1-pentanol, + 1,3-propanediol, 1-propanol and ethylene glycol in co-culture with the hydrogenotrophic + methanogen Methanothermobacter thermautotrophicus strain deltaH(T) + explanation: Names propionate explicitly as the growth substrate consumed only in + syntrophic co-culture with the H2-using methanogen, anchoring it as the central + substrate of this consortium. metals_present: - IRON - TITANIUM diff --git a/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml b/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml index e40939d3..2590889f 100644 --- a/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml +++ b/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml @@ -225,6 +225,51 @@ environmental_factors: snippet: A syntrophic propionate-oxidizing bacterium, strain MPOBT, was isolated from a culture enriched from anaerobic granular sludge explanation: Establishes ecological origin and relevance to anaerobic waste treatment processes +related_ingredients: +- preferred_term: propionate + chebi_term: + id: CHEBI:17272 + label: propionate + relevance: Propionate is the central growth substrate of this consortium. Syntrophobacter + fumaroxidans oxidizes propionate to acetate, a reaction that proceeds only when a + H2/formate-utilizing partner keeps electron-carrier concentrations low. + evidence: + - reference: doi:10.1099/00207713-48-4-1383 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: A syntrophic propionate-oxidizing bacterium, strain MPOBT, was isolated from + a + explanation: Identifies propionate as the substrate oxidized by S. fumaroxidans, the + defining metabolic activity of this syntrophy. +- preferred_term: formate + chebi_term: + id: CHEBI:15740 + label: formate + relevance: Formate is a key interspecies electron carrier transferred from S. fumaroxidans + to M. formicicum. Proteomic evidence indicates S. fumaroxidans mainly uses formate + for electron release during syntrophic growth. + evidence: + - reference: PMID:29611893 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: S. fumaroxidans mainly used formate for electron release + explanation: Anchors formate as the dominant electron-release carrier in syntrophic + propionate oxidation. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Hydrogen (dihydrogen) is the second interspecies electron carrier in this + consortium. The partner methanogen consumes the hydrogen released by S. fumaroxidans, + making propionate oxidation thermodynamically feasible. + evidence: + - reference: doi:10.1099/00207713-48-4-1383 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: It oxidized propionate syntrophically in co-culture with the hydrogen- and + formate-utilizing + explanation: Establishes hydrogen as an interspecies electron carrier consumed by the + syntrophic methanogenic partner. metals_present: - IRON metal_relevance: SIGNIFICANT diff --git a/kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml b/kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml index a6ae8d97..d92150bd 100644 --- a/kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml +++ b/kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml @@ -225,6 +225,50 @@ environmental_factors: snippet: A syntrophic propionate-oxidizing bacterium, strain MPOBT, was isolated from a culture enriched from anaerobic granular sludge explanation: Establishes ecological origin and relevance to anaerobic waste treatment processes +related_ingredients: +- preferred_term: propionate + chebi_term: + id: CHEBI:17272 + label: propionate + relevance: Central growth substrate of the consortium; Syntrophobacter fumaroxidans + oxidizes propionate to acetate via the methylmalonyl-CoA pathway, a reaction that + is thermodynamically feasible only when its H2/formate products are consumed by + the methanogenic partner. + evidence: + - reference: PMID:9828440 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: A syntrophic propionate-oxidizing bacterium, strain MPOBT, was isolated from a + explanation: Identifies propionate as the defining oxidizable substrate of strain + MPOBT (S. fumaroxidans), the primary degrader of the consortium. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: One of the two interspecies electron-transfer carriers produced by S. + fumaroxidans during propionate oxidation and consumed by the hydrogen-utilizing + methanogen M. hungatei; its low partial pressure is essential for syntrophy. + evidence: + - reference: PMID:29611893 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Special attention was put on the role of hydrogen and formate in + explanation: Anchors hydrogen (dihydrogen) as a focal electron carrier in interspecies + electron transfer during syntrophic propionate degradation. +- preferred_term: formate + chebi_term: + id: CHEBI:15740 + label: formate + relevance: The preferential interspecies electron carrier produced by S. fumaroxidans + and consumed by M. hungatei; formate transfer relieves the thermodynamic constraint + on propionate oxidation alongside H2. + evidence: + - reference: PMID:29611893 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: formate for electron release and that different confurcating mechanisms were + explanation: Identifies formate as the main electron-release carrier used by S. + fumaroxidans, central to interspecies electron transfer. metals_present: - IRON metal_relevance: SIGNIFICANT diff --git a/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml b/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml index fcb97c45..83d07ed9 100644 --- a/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml +++ b/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml @@ -302,6 +302,51 @@ external_resources: resource_id: NCBITaxon:39152 url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=39152 description: NCBI Taxonomy record for Methanococcus maripaludis. +related_ingredients: +- preferred_term: butyrate + chebi_term: + id: CHEBI:17968 + label: butyrate + relevance: > + Butyrate is the central growth substrate of the coculture; its syntrophic + beta-oxidation by S. wolfei drives the entire system. + evidence: + - reference: PMID:34603271 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: butyrate-oxidizing bacteria and methanogens + explanation: Anchors butyrate as the substrate oxidized by the bacterial partner. + - reference: doi:10.1038/s41598-018-30745-7 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: syntrophic oxidation of butyrate + explanation: Anchors butyrate as the substrate oxidized in the defined coculture. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: > + Hydrogen is the interspecies electron-carrier intermediate transferred from + the butyrate-oxidizing syntroph to the hydrogenotrophic methanogen. + evidence: + - reference: PMID:34603271 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: hydrogenotrophic methanogens + explanation: Anchors dihydrogen as the electron donor consumed by the hydrogenotrophic methanogenic partner. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: > + Methane is the terminal product of the coculture, produced by the + hydrogenotrophic methanogen during syntrophic butyrate conversion. + evidence: + - reference: doi:10.1038/s41598-018-30745-7 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: CH4production was significantly accelerated by carbon nanotubes + explanation: Anchors methane (CH4) as the gaseous product of syntrophic butyrate oxidation. associated_datasets: [] metals_present: [] rare_earth_elements_present: [] diff --git a/kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml b/kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml index 1551df5f..2986212a 100644 --- a/kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml +++ b/kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml @@ -195,6 +195,48 @@ environmental_factors: evidence_source: IN_VITRO snippet: The most rapid generation time obtained by cocultures of S explanation: Quantifies growth rate of the syntrophic consortium +related_ingredients: +- preferred_term: butyrate + chebi_term: + id: CHEBI:17968 + label: butyrate + relevance: Central growth substrate. Syntrophomonas wolfei β-oxidizes butyrate to acetate, + using protons as the electron acceptor and releasing H2; this is the entry-point substrate + that drives the entire syntrophic consortium. + evidence: + - reference: PMID:16345745 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: (butyrate through octanoate) to acetate or acetate and propionate using protons + explanation: Snippet names butyrate explicitly as the saturated fatty acid substrate β-oxidized + by S. wolfei, anchoring it as the central substrate of the consortium. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Primary oxidation product. Acetate is produced from butyrate β-oxidation by S. wolfei + and is the major reduced-carbon end product released by the fatty-acid-oxidizing partner. + evidence: + - reference: PMID:16345745 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: (butyrate through octanoate) to acetate or acetate and propionate using protons + explanation: Snippet names acetate as the direct product of fatty-acid β-oxidation, anchoring it + as a central intermediate/product of the consortium. +- preferred_term: dihydrogen + chebi_term: + id: CHEBI:18276 + label: dihydrogen + relevance: Interspecies electron carrier. H2 is the electron sink product of S. wolfei butyrate + oxidation and the substrate consumed by M. hungatei; its removal via interspecies hydrogen transfer + is thermodynamically essential to the syntrophy. + evidence: + - reference: PMID:16345745 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: as the electron acceptor (H(2) as electron sink product) + explanation: Snippet names H2 as the electron sink product of S. wolfei metabolism, anchoring + dihydrogen as the central interspecies electron carrier. metals_present: - IRON metal_relevance: SIGNIFICANT