#30 backfill: syntrophy/methanogenesis cohort batch 2 (9 communities)

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

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

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

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

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: []

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

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