Backfill related_ingredients in 7 more communities (#30)

kb/communities/East_River_Hillslope_Riparian_Transect_Community.yaml

@@ -95,6 +95,144 @@ taxonomy:
     evidence_source: COMPUTATIONAL
     snippet: all hillslope communities
     explanation: Supports hillslope communities as a compared community compartment.
+related_ingredients:
+- preferred_term: nitrate
+  chebi_term:
+    id: CHEBI:17632
+    label: nitrate
+  relevance: >
+    Nitrate is reported as a constituent of the Mancos shale bedrock underlying
+    the transect, and its availability is linked to the increased abundance of
+    Deltaproteobacteria near the weathered shale.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: the proximity to sulfate and nitrate rich Mancos shale bedrock
+    explanation: Names nitrate as a geochemical constituent of the underlying shale.
+- preferred_term: sulfate
+  chebi_term:
+    id: CHEBI:16189
+    label: sulfate
+  relevance: >
+    Sulfate is reported as a constituent of the Mancos shale bedrock and is
+    measured geochemically along the transect, consistent with the sulfate-reduction
+    metabolic potential of the riparian communities.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: the proximity to sulfate and nitrate rich Mancos shale bedrock
+    explanation: Names sulfate as a geochemical constituent of the underlying shale.
+- preferred_term: thiosulfate
+  chebi_term:
+    id: CHEBI:26977
+    label: thiosulfate
+  relevance: >
+    Thiosulfate reductase (phsA) is enriched below the water table, where it
+    reduces thiosulfate, implicating thiosulfate as a sulfur-cycle substrate in
+    the saturated floodplain sediments.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: thiosulfate reductase phsA, which catalyzes the reduction of thiosulfate to sulfite and hydrogen sulfide
+    explanation: Names thiosulfate as the substrate of an enriched reductase.
+- preferred_term: sulfite
+  chebi_term:
+    id: CHEBI:17359
+    label: sulfite
+  relevance: >
+    Sulfite is named as a product of thiosulfate reduction and as the substrate
+    of dissimilatory and anaerobic sulfite reductases active in the saturated
+    floodplain sediments.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: thiosulfate reductase phsA, which catalyzes the reduction of thiosulfate to sulfite and hydrogen sulfide
+    explanation: Names sulfite as a product of thiosulfate reduction in the sediments.
+- preferred_term: hydrogen sulfide
+  chebi_term:
+    id: CHEBI:16136
+    label: hydrogen sulfide
+  relevance: >
+    Hydrogen sulfide is named as a product of thiosulfate reduction by the
+    thiosulfate reductase enriched in below-water-table samples.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: thiosulfate reductase phsA, which catalyzes the reduction of thiosulfate to sulfite and hydrogen sulfide
+    explanation: Names hydrogen sulfide as a product of thiosulfate reduction.
+- preferred_term: methanol
+  chebi_term:
+    id: CHEBI:17790
+    label: methanol
+  relevance: >
+    Methanol dehydrogenase abundance differentiates floodplain from hillslope
+    samples, naming methanol as a substrate for aerobic oxidation in the transect.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: aerobic oxidation of methanol (which could derive from plant biomass or oxidation of methane)
+    explanation: Names methanol as a substrate of methanol dehydrogenase.
+- preferred_term: methane
+  chebi_term:
+    id: CHEBI:16183
+    label: methane
+  relevance: >
+    Methane is named as a possible source of methanol oxidized by methanol
+    dehydrogenase, linking it to the aerobic oxidative metabolic potential of the
+    community.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: aerobic oxidation of methanol (which could derive from plant biomass or oxidation of methane)
+    explanation: Names methane as a possible precursor of the oxidized methanol.
+- preferred_term: carbon monoxide
+  chebi_term:
+    id: CHEBI:17245
+    label: carbon monoxide
+  relevance: >
+    Carbon monoxide dehydrogenase abundance is higher in hillslope and above-water-table
+    samples, naming carbon monoxide as a substrate for aerobic oxidation in the transect.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: aerobic oxidation of CO (possibly produced by plants as a signaling molecule)
+    explanation: Names carbon monoxide (CO) as a substrate of CO dehydrogenase.
+- preferred_term: selenite
+  chebi_term:
+    id: CHEBI:18212
+    label: selenite(2-)
+  relevance: >
+    Selenite is named as a soluble oxidation product of shale-hosted selenium and
+    is mobilized into pore fluids, relevant to the selenium-reduction redox
+    function at depth.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: Oxidation of selenium to soluble selenite and selenate
+    explanation: Names selenite as a soluble selenium oxidation product.
+- preferred_term: selenate
+  chebi_term:
+    id: CHEBI:15075
+    label: selenate
+  relevance: >
+    Selenate is named as a soluble oxidation product of shale-hosted selenium and
+    is the substrate of selenate reductase (srdA) enriched at depth, central to the
+    transect's selenium-reduction function.
+  evidence:
+  - reference: PMID:31380022
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: Oxidation of selenium to soluble selenite and selenate
+    explanation: Names selenate as a soluble selenium oxidation product and reductase substrate.
 ecological_interactions:
 - name: Groundwater and Weathered Shale Niche Filtering
   description: Proximity to the stream, groundwater table, and weathered shale

kb/communities/Episymbiotic_CPR_DPANN_Groundwater_Community.yaml

@@ -134,6 +134,39 @@ environmental_factors:
     snippet: one agricultural and seven pristine groundwater microbial
       communities
     explanation: Supports the eight groundwater sites used in the study.
+related_ingredients:
+- preferred_term: glucose
+  chebi_term:
+    id: CHEBI:17234
+    label: glucose
+  relevance: >
+    Glucose is one of the simple intermediate metabolites whose metabolic
+    pathways are retained in the streamlined genomes of groundwater
+    Patescibacteria (CPR), centering their basic carbon metabolism.
+  evidence:
+  - reference: PMID:32252814
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: members of the Patescibacteria superphylum have retained basic metabolic
+      functions centered on glucose and pyruvate
+    explanation: Glucose named as a retained central carbon metabolite of groundwater
+      Patescibacteria.
+- preferred_term: pyruvate
+  chebi_term:
+    id: CHEBI:15361
+    label: pyruvate
+  relevance: >
+    Pyruvate is among the simple intermediate metabolites whose basic metabolic
+    pathways are retained in the reduced genomes of groundwater Patescibacteria
+    (CPR), supporting their core energy metabolism.
+  evidence:
+  - reference: PMID:32252814
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: basic metabolisms of simple intermediate metabolites such as pyruvate,
+      phosphoglycerate, and monosaccharide including glucose
+    explanation: Pyruvate named as a retained simple intermediate metabolite of
+      groundwater Patescibacteria.
 growth_media: []
 external_resources:
 - name: Primary publication for the episymbiotic CPR/DPANN groundwater community

kb/communities/Industrial_Bioreactor_Consortium.yaml

@@ -988,6 +988,101 @@ environmental_factors:
       ferriphilum, Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum,
       before adapting to a pulp density of 4%
     explanation: Links high Fe³⁺ to Ferroplasma competitive advantage
+related_ingredients:
+- preferred_term: iron(2+) sulfate
+  chebi_term:
+    id: CHEBI:75832
+    label: iron(2+) sulfate (anhydrous)
+  relevance: >
+    Ferrous sulfate is a defined energy source provided to this moderately
+    thermophilic bioleaching consortium, supplying the Fe(II) substrate oxidized
+    by iron-oxidizing members.
+  evidence:
+  - reference: PMID:24242252
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: different substrates (ferrous sulfate, elemental sulfur, and chalcopyrite)
+    explanation: Lists ferrous sulfate among the substrates serving as energy sources for the culture.
+- preferred_term: sulfur
+  chebi_term:
+    id: CHEBI:26833
+    label: sulfur atom
+  relevance: >
+    Elemental sulfur is supplied as an energy source for the sulfur-oxidizing
+    members of the consortium, which oxidize reduced sulfur to maintain the low
+    pH required for metal solubilization.
+  evidence:
+  - reference: PMID:24242252
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: different substrates (ferrous sulfate, elemental sulfur, and chalcopyrite)
+    explanation: Lists elemental sulfur among the substrates serving as energy sources.
+- preferred_term: chalcopyrite
+  chebi_term:
+    id: CHEBI:86202
+    label: chalcopyrite
+  relevance: >
+    Chalcopyrite concentrate is the primary mineral substrate bioleached by the
+    consortium, dissolved by microbially generated ferric iron to release copper.
+  evidence:
+  - reference: PMID:24242252
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: different substrates (ferrous sulfate, elemental sulfur, and chalcopyrite)
+    explanation: Lists chalcopyrite as a substrate energy source for the bioleaching culture.
+- preferred_term: copper(2+)
+  chebi_term:
+    id: CHEBI:29036
+    label: copper(2+)
+  relevance: >
+    Soluble copper released by chalcopyrite dissolution is the target product of
+    the bioleaching process and is monitored to quantify dissolution rates.
+  evidence:
+  - reference: doi:10.1007/s00253-008-1792-8
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Chalcopyrite dissolution was determined by measuring variations of soluble copper, ferric
+    explanation: Soluble copper is measured to track chalcopyrite dissolution by the consortium.
+- preferred_term: iron(3+)
+  chebi_term:
+    id: CHEBI:29034
+    label: iron(3+)
+  relevance: >
+    Ferric iron, generated by microbial Fe(II) oxidation, is the oxidant that
+    dissolves chalcopyrite; its concentration is measured to follow leaching.
+  evidence:
+  - reference: doi:10.1007/s00253-008-1792-8
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Chalcopyrite dissolution was determined by measuring variations of soluble copper, ferric
+    explanation: Ferric iron is measured to track chalcopyrite dissolution.
+- preferred_term: carbon dioxide
+  chebi_term:
+    id: CHEBI:16526
+    label: carbon dioxide
+  relevance: >
+    Carbon dioxide is supplied as an additional inorganic carbon source for
+    autotrophic members and improves bio-oxidation performance at elevated
+    temperatures.
+  evidence:
+  - reference: doi:10.3390/biology12111411
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite–arsenopyrite concentrate
+    explanation: Carbon dioxide is studied as an additional carbon source affecting bio-oxidation.
+- preferred_term: pyrite
+  chebi_term:
+    id: CHEBI:86471
+    label: pyrite
+  relevance: >
+    Pyrite is a component of the sulfide concentrate bio-oxidized by the reactor
+    consortium and serves as a sulfide mineral substrate.
+  evidence:
+  - reference: doi:10.3390/biology12111411
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite–arsenopyrite concentrate
+    explanation: Pyrite-arsenopyrite concentrate is the sulfide substrate undergoing bio-oxidation.
 metals_present:
 - COPPER
 - IRON

kb/communities/NCycle_Bioflocculation_Model_Consortium.yaml

@@ -48,6 +48,21 @@ ecological_interactions:
   scope: COMMUNITY_LEVEL
   evidence:
   - *id001
+related_ingredients:
+- preferred_term: alginate
+  chebi_term:
+    id: CHEBI:58187
+    label: alginate
+  relevance: >
+    Alginate was used as the entrapment / cell-retention matrix that promoted
+    strong nitrifier microcolony formation, a key step in building the
+    bioflocculation model consortium.
+  evidence:
+  - reference: PMID:40536564
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Alginate entrapment leads to strong microcolony formation of nitrifiers
+    explanation: Names alginate entrapment as the driver of nitrifier microcolony formation.
 environmental_factors:
 - name: oxic/anoxic sequencing batch reactor cycling
   value: Oxic/anoxic cycles and alginate entrapment were used to produce nitrifier microcolonies and mixed

kb/communities/PET_Artificial_FourSpecies_Degradation_Consortium.yaml

@@ -358,4 +358,67 @@ associated_datasets:
     evidence_source: OTHER
     snippet: This study constructed and evaluated the artificial microbial consortia in PET degradation
     explanation: Supports the supplementary material as the detailed strain and construct resource.
+related_ingredients:
+- preferred_term: poly(ethylene terephthalate) macromolecule
+  chebi_term:
+    id: CHEBI:53259
+    label: poly(ethylene terephthalate) macromolecule
+  relevance: >
+    PET is the insoluble polymer substrate that the consortium depolymerizes; PETase initiates
+    its breakdown into MHET.
+  evidence:
+  - reference: PMID:35003008
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: PET is degraded into MHET catalyzed by PETase
+    explanation: Names PET as the polymer substrate hydrolyzed by PETase.
+- preferred_term: mono(2-hydroxyethyl) terephthalate
+  relevance: >
+    MHET is the intermediate produced from PET by PETase and is further hydrolyzed by MHETase
+    into terephthalic acid and ethylene glycol.
+  evidence:
+  - reference: PMID:35003008
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: MHET is degraded into TPA and EG catalyzed by MHETase
+    explanation: Names MHET as the intermediate hydrolyzed by MHETase to TPA and EG.
+- preferred_term: terephthalic acid
+  chebi_term:
+    id: CHEBI:15702
+    label: terephthalic acid
+  relevance: >
+    Terephthalic acid (TPA) is a PET hydrolysis product whose accumulation inhibits degradation;
+    R. jostii RHA1 was added to utilize it and relieve that inhibition.
+  evidence:
+  - reference: PMID:35003008
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: R. jostii was added to reduce the inhibition caused by terephthalic acid
+    explanation: Names terephthalic acid as the inhibitory PET product utilized by R. jostii.
+- preferred_term: ethylene glycol
+  chebi_term:
+    id: CHEBI:30742
+    label: ethylene glycol
+  relevance: >
+    Ethylene glycol (EG) is the other PET hydrolysis product whose accumulation inhibits
+    degradation; P. putida KT2440 was added to consume it.
+  evidence:
+  - reference: PMID:35003008
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: reduce the inhibition caused by ethylene glycol (EG)
+    explanation: Names ethylene glycol as the inhibitory PET product consumed by P. putida.
+- preferred_term: bis(2-hydroxyethyl) terephthalate
+  chebi_term:
+    id: CHEBI:231672
+    label: bis(2-hydroxyethyl) terephthalate
+  relevance: >
+    BHET is a PET-related substrate used in degradation assays; TPA, EG, and their combination
+    inhibited its degradation by the consortium.
+  evidence:
+  - reference: PMID:35003008
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: T P A, EG and the TPA/EG combination also inhibited degradation of BHET
+    explanation: Names BHET as a substrate whose degradation is inhibited by TPA and EG.
 metal_relevance: NOT_APPLICABLE