diff --git a/kb/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.yaml b/kb/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.yaml index c2f8a3f6..b5bae056 100644 --- a/kb/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.yaml +++ b/kb/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.yaml @@ -219,6 +219,61 @@ environmental_factors: evidence_source: IN_VIVO snippet: in combination under 3 dietary conditions explanation: Supports diet as a controlled environmental factor. +related_ingredients: +- preferred_term: acetate + chebi_term: + id: CHEBI:30089 + label: acetate + relevance: Acetate is the cross-feeding currency between B. thetaiotaomicron + and E. rectale in this gnotobiotic model — B. theta produces acetate + that E. rectale consumes to generate butyrate. Cecal acetate is + significantly lower in cocolonised mice, confirming the in vivo cross- + feeding; any environment-analog medium must support an acetate gradient + rather than a fixed pool. + evidence: + - reference: PMID:19321416 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: cecal acetate levels are significantly lower in cocolonized + mice compared with B. thetaiotaomicron monoassociated animals + explanation: Anchors acetate as the in vivo cross-feeding intermediate + whose pool shifts predictably when E. rectale is added to the + community. +- preferred_term: butyrate + chebi_term: + id: CHEBI:17968 + label: butyrate + relevance: Butyrate is the SCFA output of the consortium and the + epithelium-relevant endpoint; cecal butyrate levels stay similar between + E. rectale mono- and biassociated mice, indicating the coculture + maintains butyrate flux on a smaller acetate pool — a key behavior any + cultivation medium must support measuring. + evidence: + - reference: PMID:19321416 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: cecal butyrate levels are similar in E. rectale mono- and + biassociated animals + explanation: Anchors butyrate as the maintained-flux output that + distinguishes this coculture from monocolonised controls. +- preferred_term: host-derived mucin glycans + chebi_term: + id: CHEBI:24400 + label: glycoprotein + relevance: Mucin glycans are the host-derived substrate that B. theta + up-regulates when E. rectale is present — switching its glycan usage + away from what E. rectale also exploits. Any defined medium for this + coculture should include a mucin glycan source (or its surrogates) so + that the strain-level adaptation is reproducible. + evidence: + - reference: PMID:19321416 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: B. thetaiotaomicron adapts to the presence of E. rectale by + up-regulating a variety of loci specific for host-derived mucin + glycans that E. rectale is unable to use + explanation: Anchors host-derived mucin glycans as the niche-partitioning + substrate whose use is selected by the coculture context. associated_datasets: - name: Exact-composition publication - Bacteroides thetaiotaomicron VPI-5482 and Eubacterium rectale ATCC 33656 dataset_type: PHENOTYPE diff --git a/kb/communities/Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community.yaml b/kb/communities/Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community.yaml index 3a1e2762..cc5ea81b 100644 --- a/kb/communities/Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community.yaml +++ b/kb/communities/Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community.yaml @@ -147,6 +147,43 @@ environmental_factors: and base) in young Brachypodium distachyon explanation: Supports the spatial zone sampling design. growth_media: [] +related_ingredients: +- preferred_term: root exudates + chebi_term: + id: CHEBI:46662 + label: organic matter + relevance: Root exudates differ across the developing primary root (tip vs + base) and define the labile-carbon source that distinguishes the + rhizosphere niche from bulk soil; an environment-analog medium must + supply a tip-vs-base-distinguishable exudate mixture, not a uniform + background. + evidence: + - reference: PMID:37280433 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Root exudation patterns are known to vary along distinct parts + of the root even in juvenile plants giving rise to spatially distinct + microbial niches + explanation: Anchors variable root exudation as the substrate gradient + generating the spatially distinct rhizosphere niches sampled in the + EcoFAB design. +- preferred_term: labile root carbon + chebi_term: + id: CHEBI:46662 + label: organic matter + relevance: The absence of easily available, labile carbon and nutrients + in bulk soil — as opposed to the labile pool concentrated near roots — + is the explicit functional contrast the paper identifies; any + cultivation medium for this rhizosphere community must supply a + labile-carbon-rich phase distinct from a nutrient-limited control. + evidence: + - reference: PMID:37280433 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: the absence of easily available, labile carbon and nutrients + in bulk soil relative to roots + explanation: Anchors labile root carbon as the dimension separating + rhizosphere from bulk-soil microbial function. external_resources: - name: Primary publication for the Brachypodium young-root rhizosphere community repository: OTHER diff --git a/kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml b/kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml index 50aaca0b..dfc7b818 100644 --- a/kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml +++ b/kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml @@ -192,6 +192,58 @@ external_resources: resource_id: doi:10.1111/1758-2229.70261 url: https://doi.org/10.1111/1758-2229.70261 description: DOI link to the Environmental Microbiology Reports paper. +related_ingredients: +- preferred_term: chalcopyrite + chebi_term: + id: CHEBI:50885 + label: chalcopyrite + relevance: Chalcopyrite (CuFeS2) is the primary copper-sulphide ore the + Cyprus consortium was enriched on; an environment-analog cultivation + medium would need chalcopyrite (or a soluble Cu(II)+Fe(II)+sulphide + surrogate) as the central solid substrate driving consortium + composition and surface attachment. + evidence: + - reference: PMID:41381092 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Copper bioleaching is a green technology for the recovery of + copper from chalcopyrite (CuFeS2) and chalcocite (Cu2S) ores + explanation: Anchors chalcopyrite (the Cu(II)/Fe(II) sulphide source + species) as the central substrate of this bioleaching consortium. +- preferred_term: chalcocite + chebi_term: + id: CHEBI:33415 + label: copper(I) sulfide + relevance: Chalcocite (Cu2S) was the second mineral the consortium was + sub-cultured to; switching between chalcopyrite and chalcocite is what + the study used to investigate how community composition responds to + mineral structure and the absence of mineral-derived Fe, so a medium + designed to recapitulate that experiment needs both phases. + evidence: + - reference: PMID:41381092 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: established a microbial consortium from a copper bioleaching + column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite + explanation: Anchors chalcocite as the second mineral substrate used to + probe consortium dependence on mineral-derived Fe. +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: Mineral-derived Fe (released from chalcopyrite into solution as + Fe(II)) is the explicit variable the study manipulated by switching to + chalcocite (which lacks Fe); Fe(II) is the substrate for Leptospirillum + ferrodiazotrophum and Acidithiobacillus iron-oxidisers central to the + consortium. + evidence: + - reference: PMID:41381092 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: to investigate how the community composition shifts due to + changes in mineral structure and the absence of mineral-derived Fe + explanation: Anchors mineral-derived Fe(II) as the controllable substrate + whose absence (in chalcocite enrichments) restructures the consortium. associated_datasets: [] metals_present: - COPPER diff --git a/kb/communities/Ewaste_Bioleaching_Consortium.yaml b/kb/communities/Ewaste_Bioleaching_Consortium.yaml index bccc9e3a..77b07662 100644 --- a/kb/communities/Ewaste_Bioleaching_Consortium.yaml +++ b/kb/communities/Ewaste_Bioleaching_Consortium.yaml @@ -563,6 +563,40 @@ environmental_factors: snippet: the inhibiting effect of PCBs limited the microbial activity by delaying the onset of the exponential iron oxidation explanation: Documents PCB-driven inhibition of microbial activity through delayed onset of exponential iron oxidation. +related_ingredients: +- preferred_term: glycine + chebi_term: + id: CHEBI:15428 + label: glycine + relevance: Glycine is the substrate fed at 10 g/L to P. putida WCS361 to + drive cyanide production at 21.5 mg/L; a two-step bioleaching medium + for this consortium must include glycine at the cyanide-induction + concentration to enable the gold-mobilization step. + evidence: + - reference: PMID:26704063 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: 21.5 (±1.5)mg/L cyanide with 10g/L glycine as the substrate + explanation: Anchors glycine at 10 g/L as the curator-supported substrate + for cyanide biosynthesis in the second bioleaching step. +- preferred_term: cyanide + chebi_term: + id: CHEBI:17514 + label: cyanide + relevance: Cyanide is the gold-complexing lixiviant produced by + P. fluorescens / P. putida in the second bioleaching step; the medium + has to be designed so cyanide accumulates to alkaline-stage + concentrations (~21.5 mg/L) without inhibiting the heterotrophic + Pseudomonas producers. + evidence: + - reference: PMID:26704063 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: cyanide-producing heterotrophic Pseudomonas fluorescens and + Pseudomonas putida were used + explanation: Anchors cyanide production by the second-step Pseudomonas + members of the consortium; the abstract goes on to identify cyanide + as the gold-complexing agent in the subsequent step. metals_present: - COPPER - GOLD diff --git a/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml b/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml index fa042eba..4c01c492 100644 --- a/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml +++ b/kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml @@ -469,6 +469,39 @@ environmental_factors: of the response surface methodologies (RSM) which yielded optimal performance at 80 min contact time, pH 9.0, and 0.15 g L-1 ZMR dose, achieving 98.84 % Cr(VI) removal explanation: Quantifies organic matter stress condition +related_ingredients: +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: Fe(II) is the principal energy substrate for the ferrous-iron + oxidising Ferroplasma acidiphilum and partner Leptospirillum + iron-oxidisers; any environment-analog cultivation medium for this + syntrophic pair must supply Fe(II) at extremely low pH. + evidence: + - reference: PMID:16104851 + supports: SUPPORT + evidence_source: REVIEW + snippet: acidophilic, ferrous-iron oxidizing Ferroplasma acidiphilum + explanation: Anchors Fe(II) oxidation as the defining energy metabolism + of Ferroplasma in the syntrophic consortium. +- preferred_term: pyrite + chebi_term: + id: CHEBI:46627 + label: pyrite + relevance: Pyrite (FeS2) and related sulphide ores are the upstream + substrate that releases Fe(II) and sulphide species into the + Ferroplasma-Leptospirillum habitat; a cultivation medium that + recapitulates the syntrophy needs a pyrite-class mineral substrate or + a soluble surrogate. + evidence: + - reference: PMID:16104851 + supports: SUPPORT + evidence_source: REVIEW + snippet: able to mobilize metals from sulfide ores, e.g. pyrite, + arsenopyrite and copper-containing sulfides + explanation: Anchors pyrite (and the sulfide-ore class) as the upstream + substrate the Ferroplasma-led consortium mobilises. metals_present: - COPPER - IRON diff --git a/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml b/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml index 5bc239ae..a6739445 100644 --- a/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml +++ b/kb/communities/Iberian_Pit_Lake_Stratified_Community.yaml @@ -722,6 +722,59 @@ environmental_factors: a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling explanation: Quantifies diversity increase with depth +related_ingredients: +- preferred_term: sulfate + chebi_term: + id: CHEBI:16189 + label: sulfate + relevance: Sulfate is the quantitatively dominant anion in the Iberian + Pyrite Belt pit lakes — present at high concentrations alongside + dissolved heavy metals — and is the central electron-acceptor pool + structuring the acidic stratified community; an environment-analog + medium must supply sulfate at concentrations matching the IPB regime. + evidence: + - reference: PMID:23840525 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Both pit lakes are acidic and showed high concentrations of + sulfate and dissolved metals + explanation: Anchors sulfate as the central anion of the pit lake + hydrochemistry. +- preferred_term: iron(2+) + chebi_term: + id: CHEBI:29033 + label: iron(2+) + relevance: Fe(II) is the substrate the IPB iron-oxidising bacteria + (Leptospirillum, Acidithiobacillus ferrooxidans) consume in the upper + oxic layers; a cultivation medium for the oxidising guild must supply + Fe(II) at low pH. + evidence: + - reference: PMID:23840525 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: iron oxidizing bacteria (Leptospirillum, Acidithiobacillus + ferrooxidans) and facultative iron reducing bacteria and archaea + explanation: Anchors Fe(II) oxidation as one half of the redox axis + structuring the stratified pit lake community. +- preferred_term: iron(3+) + chebi_term: + id: CHEBI:29034 + label: iron(3+) + relevance: Fe(III) — produced by upper-layer oxidisers — is the electron + acceptor the facultative iron-reducers (Acidiphilium, Ferroplasma, + Acidithiobacillus ferrooxidans in reducing mode) in the bottom layer + consume, closing the iron cycle across the chemocline; the medium + needs both oxidation states available to recapitulate the stratified + redox structure. + evidence: + - reference: PMID:23840525 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: facultative iron reducing bacteria and archaea + (Acidithiobacillus ferrooxidans, Acidiphilium, Actinobacteria, + Acidimicrobiales, Ferroplasma) detected in the bottom layer + explanation: Anchors Fe(III) reduction as the bottom-layer half of the + redox axis closing the stratified iron cycle. metals_present: - COPPER - IRON diff --git a/kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml b/kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml index 5341e8a4..57010877 100644 --- a/kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml +++ b/kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml @@ -497,6 +497,25 @@ environmental_factors: snippet: The membership and relative abundances of the strains stabilized after around 5 growth cycles and resulted in just a few dominant strains that depended on the medium explanation: Documents the timeframe to stable community structure +related_ingredients: +- preferred_term: glucose + chebi_term: + id: CHEBI:17234 + label: glucose + relevance: Glucose is the central carbon source for the minimal-medium + arm of this passaging study; the community-assembly outcome is + explicitly different between complex and minimal-glucose media, so a + medium designed to recapitulate this Populus PD10 community must define + the glucose-vs-complex axis as a primary independent variable. + evidence: + - reference: PMID:33995895 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: co-cultured in either complex or minimal glucose media and + serially transferred until a stable community structure formed + explanation: Anchors glucose as the defining minimal-medium carbon + source under which a distinct stable consortium emerges from the + same 10-strain inoculum. associated_datasets: - name: Populus PD10 16S rRNA gene amplicon data dataset_type: AMPLICON_16S