#30 backfill batch 2: 4 metals + 3 gut/rhizosphere communities (#83)

* #30 backfill batch 2: 4 metals + 3 gut/rhizosphere communities

Continues the SPRUCE/wetland dogfood pattern from PRs #79/#80/#81. Each
entry uses CHEBI terms with snippets taken verbatim from cached
PMID/DOI abstracts; no cross-repo IDs (MIM IDs haven't been minted).

AMD/biomining/REE (4 of 16 remaining):

| Community | Ingredients | Source |
|---|---|---|
| Cyprus_Copper_Sulphide_Bioleaching_Consortium | chalcopyrite (Cu(II) surrogate), chalcocite (Cu(I) sulfide), iron(2+) | PMID:41381092 |
| Ferroplasma_Leptospirillum_Syntrophy | iron(2+), pyrite | PMID:16104851 |
| Iberian_Pit_Lake_Stratified_Community | sulfate, iron(2+) | PMID:23840525 |
| Ewaste_Bioleaching_Consortium | glycine (10 g/L cyanide substrate), hydrogen cyanide (gold lixiviant) | PMID:26704063 |

Gut/rhizosphere (3 of ~13 remaining):

| Community | Ingredients | Source |
|---|---|---|
| Bacteroides_Eubacterium_Gnotobiotic_Gut_Model | acetate, butyrate, host-derived mucin glycans | PMID:19321416 |
| Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community | root exudates, labile root carbon | PMID:37280433 |
| ORNL_PMI_Populus_PD10_SynCom | glucose (minimal-medium axis) | PMID:33995895 |

#30 related_ingredients adoption: 12/265 -> 19/265.

Test plan: just test (136 passed), all 7 modified files validate
clean against the schema.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* Address Copilot review on #83

Five findings, all valid:

1. Cyprus chalcopyrite was mapped to CHEBI:30074 / "copper(2+)", which
   is wrong on both axes. Updated to CHEBI:50885 / "chalcopyrite" —
   the mapping the repo already uses (Copper_Biomining_Heap_Leach
   metabolites).

2. Ewaste cyanide entry's `chebi_term.label` said "hydrogen cyanide"
   but CHEBI:17514's canonical label is "cyanide". Aligned label.

3. Ewaste cyanide entry's snippet ("This gold complexing agent was
   used…") did not literally mention cyanide. Replaced with the more
   direct adjacent abstract sentence ("cyanide-producing heterotrophic
   Pseudomonas fluorescens and Pseudomonas putida were used") and
   moved the gold-complexing context into the explanation field.

4. Iberian Pit Lake relevance text described an Fe(II)/Fe(III) cycle
   across the chemocline but only iron(2+) was listed. Added a
   separate iron(3+) related_ingredient with its own snippet
   anchoring the bottom-layer iron-reducing guild
   (Acidiphilium / Ferroplasma / Acidithiobacillus ferrooxidans in
   reducing mode); split the original Fe(II) relevance text to
   reference only the oxidising guild.

5. Ewaste "gold-mobilisation" -> "gold-mobilization" for spelling
   consistency with the rest of the repo (American spelling).

136 tests still pass; all 3 modified YAMLs validate clean.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: realmarcin

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

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

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

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

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

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

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