diff --git a/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml b/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml index 2a76d59c..c72f4b50 100644 --- a/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml +++ b/kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml @@ -52,3 +52,34 @@ environmental_factors: description: Plant mutants deficient in secreted phytoalexins, flavonoids, and coumarins. evidence: - *id001 +related_ingredients: +- preferred_term: coumarin + chebi_term: + id: CHEBI:28794 + label: coumarin + relevance: Coumarins are the central class of root-exuded specialized metabolites + studied in this SynCom; loss of coumarin biosynthesis in the f6'h1 mutant drives + the iron-dependent shift in root-associated bacterial community composition. + evidence: + - reference: PMID:31152139 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: lack of coumarin biosynthesis in f6'h1 mutant plant lines causes a shift + in the root microbial community specifically under iron deficiency + explanation: Names coumarin biosynthesis as the perturbation that reshapes the + synthetic root microbiome, anchoring coumarin as central to this community. +- preferred_term: iron(3+) + chebi_term: + id: CHEBI:29034 + label: iron(3+) + relevance: Iron availability gates the community effect; the coumarins exuded by + Arabidopsis act as iron-mobilizing molecules that sculpt the bacterial community + under iron-limited conditions, making ferric iron a defining environmental driver. + evidence: + - reference: PMID:31152139 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: iron-mobilizing coumarins in sculpting the A. thaliana root bacterial + community + explanation: Links iron mobilization by coumarins to community structuring, anchoring + ferric iron as a central species in this iron-deficiency-dependent system. diff --git a/kb/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.yaml b/kb/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.yaml index 4087f186..fb44cbc2 100644 --- a/kb/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.yaml +++ b/kb/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.yaml @@ -194,6 +194,22 @@ environmental_factors: plant growth explanation: Supports the time-course sampling design. growth_media: [] +related_ingredients: +- preferred_term: 13CO2 (plant-fixed carbon source) + chebi_term: + id: CHEBI:16526 + label: carbon dioxide + relevance: 13CO2 is the labeled substrate at the center of this community's SIP + design; Avena fatua fixed 13CO2 photosynthetically and routed the labeled + carbon into root exudates and the rhizosphere food web, allowing 13C-enriched + bacteria, microeukaryotes, and phage to be tracked. + evidence: + - reference: PMID:34468166 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: carbon from Avena fatua grown in a 13CO2 atmosphere + explanation: Anchors carbon dioxide as the 13C-labeled atmospheric substrate + whose fixed carbon is traced into the rhizosphere community. external_resources: - name: Primary publication for the Avena rhizosphere cross-kingdom SIP community repository: OTHER diff --git a/kb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml b/kb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml index 40db065c..eca56fc0 100644 --- a/kb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml +++ b/kb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml @@ -182,6 +182,63 @@ environmental_factors: evidence_source: IN_VIVO snippet: fermentation of dietary fructans to acetate explanation: Supports dietary fructans as a substrate shaping the interaction. +related_ingredients: +- preferred_term: formate + chebi_term: + id: CHEBI:15740 + label: formate + relevance: Formate produced by Bacteroides thetaiotaomicron is the key cross-fed substrate + transferred to Methanobrevibacter smithii, which consumes it for methanogenesis. This + interspecies transfer is the metabolic basis of the gnotobiotic mutualism. + evidence: + - reference: PMID:16782812 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: B. thetaiotaomicron-derived formate is used by M. smithii for methanogenesis + explanation: Snippet names formate explicitly as the B. thetaiotaomicron-derived substrate + feeding M. smithii methanogenesis. +- preferred_term: methane + chebi_term: + id: CHEBI:16183 + label: methane + relevance: Methane is the terminal product of M. smithii methanogenesis fueled by + B. thetaiotaomicron-derived formate, representing the metabolic sink that drives the + syntrophic interaction in the mouse gut. + evidence: + - reference: PMID:16782812 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: B. thetaiotaomicron-derived formate is used by M. smithii for methanogenesis + explanation: Snippet anchors methanogenesis, the methane-producing process for which + methane is the defining product. +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Acetate is the major fermentation product that M. smithii directs B. thetaiotaomicron + to produce from dietary fructans, marking the methanogen-specific shift in bacterial + metabolic output. + evidence: + - reference: PMID:16782812 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: M. smithii directs B. thetaiotaomicron to focus on fermentation of dietary fructans to acetate + explanation: Snippet names acetate as the end product of the methanogen-directed fructan + fermentation. +- preferred_term: fructan + chebi_term: + id: CHEBI:28796 + label: fructan + relevance: Dietary fructans are the central polysaccharide substrate whose fermentation by + B. thetaiotaomicron is redirected by M. smithii, linking dietary carbohydrate input to the + acetate-formate-methane syntrophy. + evidence: + - reference: PMID:16782812 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: fermentation of dietary fructans to acetate + explanation: Snippet names dietary fructans as the substrate whose fermentation underlies + the interaction. associated_datasets: - name: Methanobrevibacter smithii gene sequences dataset_type: GENOME diff --git a/kb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml b/kb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml index 97471db3..c5674c66 100644 --- a/kb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml +++ b/kb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml @@ -258,6 +258,53 @@ ecological_interactions: microbiota of infants. explanation: Supports that Bacteroides species contribute to authentic infant gut microbiota characteristics including HMO degradation. +related_ingredients: +- preferred_term: human milk oligosaccharide + chebi_term: + id: CHEBI:50699 + label: oligosaccharide + relevance: Human milk oligosaccharides are the defining growth substrate of BIG-Syc. + They are degraded by the primary Bifidobacterium and Bacteroides degraders, and the + specific four- versus five-HMO mix determines whether B. infantis or B. bifidum + dominates the community. + evidence: + - reference: doi:10.1093/ismejo/wrae209 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: human milk oligosaccharides prompt resource-sharing for their complete degradation + while leading to a different compositional and functional profile in the community + explanation: Anchors human milk oligosaccharides (oligosaccharides) as the central + substrate driving resource-sharing and community structure. +- preferred_term: organic acid + chebi_term: + id: CHEBI:64709 + label: organic acid + relevance: Organic acids are the cross-fed metabolites released by HMO degraders and + consumed by the cross-feeding members of BIG-Syc, central to the syntrophic teamwork + that achieves complete HMO degradation. + evidence: + - reference: doi:10.1093/ismejo/wrae209 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: BIG-Syc demonstrated teamwork as cross-feeders utilized simpler carbohydrates, + organic acids, and gases released from human milk oligosaccharide degraders. + explanation: Anchors organic acids as cross-fed products that cross-feeders consume + from the HMO degraders. +- preferred_term: carbohydrate + chebi_term: + id: CHEBI:16646 + label: carbohydrate + relevance: Simpler carbohydrates liberated from HMO breakdown are a key shared resource + in BIG-Syc, taken up by cross-feeders that cannot degrade intact human milk + oligosaccharides themselves. + evidence: + - reference: doi:10.1093/ismejo/wrae209 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: BIG-Syc demonstrated teamwork as cross-feeders utilized simpler carbohydrates, + organic acids, and gases released from human milk oligosaccharide degraders. + explanation: Anchors simpler carbohydrates as the HMO-derived shared resource utilized + by cross-feeders. associated_datasets: - name: BioModels model archive dataset_type: OTHER diff --git a/kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml b/kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml index 574b3d31..9d40deab 100644 --- a/kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml +++ b/kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml @@ -218,4 +218,20 @@ associated_datasets: evidence_source: IN_VITRO snippet: strain-specific quantitative PCR explanation: Supports the publication as the source of strain-resolved consortium measurements. +related_ingredients: +- preferred_term: amino acid + chebi_term: + id: CHEBI:33709 + label: amino acid + relevance: Amino acids are the central exchanged substrate of this engineered consortium. + Each of the four strains was made auxotrophic for three amino acids while overproducing one, + so reciprocal amino acid exchange is the designed mechanism driving cross-feeding and the + observed increase in population evenness. + evidence: + - reference: doi:10.1128/mSystems.00352-19 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Each strain is auxotrophic for three amino acids and overproduces one + explanation: Anchors amino acids as the auxotrophy-complementing, overproduced compounds exchanged + between strains in the engineered consortium. metal_relevance: NOT_APPLICABLE diff --git a/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml b/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml index 58030292..b022af1f 100644 --- a/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml +++ b/kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml @@ -47,6 +47,22 @@ ecological_interactions: scope: COMMUNITY_LEVEL evidence: - *id001 +related_ingredients: +- preferred_term: antibiotics + chebi_term: + id: CHEBI:33282 + label: antibacterial agent + relevance: Antibiotics are one of the explicitly named classes of exometabolites assayed + from the shared reservoir in this Transwell synthetic community, representing chemically + mediated antagonistic interactions among physically separated community members. + evidence: + - reference: PMID:29152587 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: antibiotics, are assayed from the reservoir using sensitive mass spectrometry. + explanation: The snippet names antibiotics as one of the exometabolite classes assayed + from the shared reservoir, anchoring the antibacterial agent compound class as a central + exchanged exometabolite in this community. environmental_factors: - name: defined synthetic community design value: Synthetic community members are cultured in a filter plate system that separates cells while diff --git a/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml b/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml index dfb9d802..04e624c7 100644 --- a/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml +++ b/kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml @@ -53,3 +53,20 @@ environmental_factors: description: In vitro exposure to MBOA, a maize benzoxazinoid breakdown product. evidence: - *id001 +related_ingredients: +- preferred_term: MBOA (6-methoxybenzoxazolin-2(3H)-one) + chebi_term: + id: CHEBI:195240 + label: 6-methoxy-2-benzoxazolinone + relevance: MBOA is the maize benzoxazinoid breakdown product the SynComs were exposed + to in vitro; the benzoxazinoid-metabolizing community redirects MBOA degradation + toward an acetamide and can use MBOA as a sole carbon source, making it the central + compound shaping community composition and function. + evidence: + - reference: PMID:40853002 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: We exposed both communities to the benzoxazinoid MBOA (6-methoxybenzoxazolin-2(3H)-one) + in vitro + explanation: Names MBOA explicitly with its full chemical name (6-methoxybenzoxazolin-2(3H)-one), + anchoring it as the benzoxazinoid the SynComs metabolize. diff --git a/kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml b/kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml index 5b0ae0b1..594b80bb 100644 --- a/kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml +++ b/kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml @@ -306,6 +306,66 @@ growth_media: evidence_source: IN_VITRO snippet: the eight bacterial species were cultivated individually for 72 h before inoculation explanation: Supports the preparation of individual strains before community inoculation. +related_ingredients: +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Acetate is a central short-chain fatty acid in SIHUMIx community metabolism; + metabolic modelling of the eight-species community predicts acetate as a cross-fed + product exchanged between Blautia producta and other members under complex intestinal + medium conditions. + evidence: + - reference: PMID:33622394 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: production of the short-chain fatty acid acetate + explanation: Names acetate explicitly as a short-chain fatty acid produced within + the SIHUMIx community metabolism. +- preferred_term: butyrate + chebi_term: + id: CHEBI:17968 + label: butyrate + relevance: Butyrate is a key short-chain fatty acid output of SIHUMIx, produced by + its butyrogenic members; its concentration is a primary functional readout that + shifts when colonic transit time is altered in bioreactor cultivation. + evidence: + - reference: doi:10.3390/microorganisms7120641 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: a reduction in butyrate, methyl butyrate, isobutyrate, valerate, and isovalerate + concentrations + explanation: Identifies butyrate as a measured short-chain fatty acid output of + the SIHUMIx community that responds to transit-time perturbation. +- preferred_term: carbohydrate + chebi_term: + id: CHEBI:16646 + label: carbohydrate + relevance: Carbohydrates are the principal dietary substrates fermented by SIHUMIx; + carbohydrate metabolism is a core community function that decreases as colonic + transit time is shortened in the in vitro model. + evidence: + - reference: doi:10.3390/microorganisms7120641 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: a slight decrease in glycan biosynthesis, carbohydrate, and amino acid + metabolism + explanation: Anchors carbohydrate metabolism as a central, measurable substrate-utilization + function of the SIHUMIx community. +- preferred_term: choline + chebi_term: + id: CHEBI:15354 + label: choline + relevance: Choline is an exchanged metabolite in SIHUMIx community metabolism; community + modelling predicts increased choline uptake by Blautia producta coupled to betaine + production, illustrating substrate cross-feeding within the eight-species model. + evidence: + - reference: PMID:33622394 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the uptake of choline along with the production of betaine was increased + explanation: Names choline as a substrate taken up by a SIHUMIx member during predicted + community metabolic exchange. associated_datasets: - name: SIHUMIx metaproteomics and metatranscriptomics study dataset_type: METAPROTEOME