From 838ff6700847b05a7baef0139b0f9ca6cd6075df Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Thu, 28 May 2026 21:33:45 -0700 Subject: [PATCH] #30 backfill: gut/rhizosphere cohort batch 2 (5 communities) Continues the gut/rhizosphere arm of the #30 related_ingredients backfill. Every entry uses a CHEBI term verified live against the ChEBI sqlite db via OAK, with snippets copied verbatim from cached PMID/DOI abstracts. No cross-repo IDs. related_ingredients adoption: 41/265 -> 46/265. | Community | Ingredients (CHEBI-verified) | |---|---| | Tomato_Oxylipin_SynCom3 | oxylipin, colneleic acid, colnelenic acid | | Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota | glucose, triglyceride | | Honeybee_Core20_Defined_Microbiota | carbohydrate, phosphoenolpyruvate | | Soybean_N_Fixation_sfSynCom | N-acyl-L-homoserine lactone | | Medicago_Nodule_Biofertilizer_SynCom | dinitrogen | Batch B also screened OMM12, hCom2, and Altered_Schaedler_Flora, but their only cached references are stubs (title + prior snippets, no abstract body), so no verbatim-supportable ingredient exists; left unchanged rather than inventing snippets. They need full abstracts re-fetched into references_cache first. Pre-existing CHEBI bug flagged (out of scope): Soybean_N_Fixation metabolites use CHEBI:48850 for "N-acyl-L-homoserine lactone", but that id is alkyloxynaphthalene; correct id is CHEBI:55474 (used in the new block). Test plan: just test (136 passed, 9 skipped), all 5 files validate clean. Co-Authored-By: Claude Opus 4.8 (1M context) --- ...iveSpecies_Gnotobiotic_Gut_Microbiota.yaml | 27 +++++++++++ .../Honeybee_Core20_Defined_Microbiota.yaml | 31 +++++++++++++ .../Medicago_Nodule_Biofertilizer_SynCom.yaml | 17 +++++++ .../Soybean_N_Fixation_sfSynCom.yaml | 20 ++++++++ kb/communities/Tomato_Oxylipin_SynCom3.yaml | 46 +++++++++++++++++++ 5 files changed, 141 insertions(+) diff --git a/kb/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.yaml b/kb/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.yaml index 0eba9243..e2e0dff1 100644 --- a/kb/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.yaml +++ b/kb/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.yaml @@ -222,6 +222,33 @@ growth_media: evidence_source: IN_VITRO snippet: All bacteria were maintained on MMRS medium at 30 explanation: Supports modified MRS and incubation temperature for bacterial propagation. +related_ingredients: +- preferred_term: glucose + chebi_term: + id: CHEBI:17234 + label: glucose + relevance: Host glucose is a central nutritional readout of this five-species community; the + yeast-glucose diet supplies glucose and colonization by any of the five bacterial taxa lowers + host glucose content relative to axenic flies. + evidence: + - reference: PMID:24242251 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: The low glucose content of conventional flies was recapitulated in gnotobiotic Drosophila flies colonized with any of the 5 bacterial taxa tested. + explanation: The snippet names glucose as the host metabolite directly modulated by colonization with members of this defined community. +- preferred_term: triglyceride + chebi_term: + id: CHEBI:17855 + label: triglyceride + relevance: Host triglyceride content is a key nutrient-allocation phenotype of this community; only + flies carrying both Acetobacter and Lactobacillus members restore triglyceride to conventional + levels, making triglyceride central to the Acetobacter-Lactobacillus interaction. + evidence: + - reference: PMID:24242251 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Only flies with both Acetobacter and Lactobacillus had triglyceride contents restored to the level in conventional flies. + explanation: The snippet anchors triglyceride as the host lipid metabolite whose level depends on the combined bacterial members of this community. associated_datasets: - name: Exact-composition publication - Drosophila five-species gnotobiotic microbiota dataset_type: PHENOTYPE diff --git a/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml b/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml index b242bee4..fc839cf7 100644 --- a/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml +++ b/kb/communities/Honeybee_Core20_Defined_Microbiota.yaml @@ -57,3 +57,34 @@ environmental_factors: inhibition. evidence: - *id001 +related_ingredients: +- preferred_term: carbohydrate + chebi_term: + id: CHEBI:16646 + label: carbohydrate + relevance: Carbohydrate utilization is a defining functional capacity of the Core-20 community, + enriched in the genomic analysis of the defined microbiota and likely central to its colonization + and immune-priming activity in the honeybee gut. + evidence: + - reference: PMID:36532452 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: Functions related to carbohydrate utilization and the phosphoenolpyruvate-dependent sugar + phosphotransferase system (PTS systems) are represented in genomic analysis of the defined community + explanation: The abstract names carbohydrate utilization as a represented function of the Core-20 + community, anchoring carbohydrate as a central substrate class. +- preferred_term: phosphoenolpyruvate + chebi_term: + id: CHEBI:18021 + label: phosphoenolpyruvate + relevance: The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is represented in + the Core-20 genomes, implicating phosphoenolpyruvate as the central phosphoryl donor driving sugar + uptake in this gut community. + evidence: + - reference: PMID:36532452 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS systems) are represented + in genomic analysis of the defined community + explanation: The abstract explicitly names the phosphoenolpyruvate-dependent PTS as a represented + function, anchoring phosphoenolpyruvate as a key metabolite in sugar transport. diff --git a/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml b/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml index 86195564..9e6f2f80 100644 --- a/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml +++ b/kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml @@ -64,3 +64,20 @@ environmental_factors: description: Metal contamination, salinity, drought, and high temperature in estuarine soils. evidence: - *id001 +related_ingredients: +- preferred_term: dinitrogen + chebi_term: + id: CHEBI:17997 + label: dinitrogen + relevance: Atmospheric dinitrogen (N2) is the substrate fixed by the Ensifer (rhizobial) + members of this Medicago nodule SynCom. Inoculation increased plant nitrogen content up + to 4-fold under metal stress, the central nutritional benefit of this nodule biofertilizer. + evidence: + - reference: PMID:37299063 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: nodulation (from 1.5- to 3-fold increase in nodules number), photosynthesis and + nitrogen content (up to 4-fold under metal stress) under all the controlled conditions + tested + explanation: The increase in nodulation and plant nitrogen content reflects symbiotic + dinitrogen fixation by the nodule-forming rhizobial members of the SynCom. diff --git a/kb/communities/Soybean_N_Fixation_sfSynCom.yaml b/kb/communities/Soybean_N_Fixation_sfSynCom.yaml index 40d1ded4..3c9c80aa 100644 --- a/kb/communities/Soybean_N_Fixation_sfSynCom.yaml +++ b/kb/communities/Soybean_N_Fixation_sfSynCom.yaml @@ -445,6 +445,26 @@ environmental_factors: dependence on synthetic nitrogen fertilizers ' +related_ingredients: +- preferred_term: N-acyl-L-homoserine lactone + chebi_term: + id: CHEBI:55474 + label: N-acyl-L-homoserine lactone + relevance: Acyl homoserine lactones (AHLs) are the central signaling metabolites + produced by the two Pantoea helper strains in this sfSynCom. They drive the quorum + sensing interaction that significantly enhances colonization and infection of + soybean roots by the core symbiont Bradyrhizobium elkanii BXYD3, which is the + mechanistic basis for the community's improved nodulation and nitrogen fixation. + evidence: + - reference: PMID:40052412 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Two of these helper strains assigned to the Pantoea taxon produce acyl + homoserine lactones, which significantly enhanced the colonization and infection + of soybean by BXYD3 + explanation: The snippet names acyl homoserine lactones as the compound produced + by the Pantoea helper strains, directly anchoring N-acyl-L-homoserine lactone + as the key signaling metabolite of this community. metals_present: [] metal_relevance: INCIDENTAL metal_notes: Metal/REE detected via environmental factor measurements diff --git a/kb/communities/Tomato_Oxylipin_SynCom3.yaml b/kb/communities/Tomato_Oxylipin_SynCom3.yaml index d538ed86..6bec1f07 100644 --- a/kb/communities/Tomato_Oxylipin_SynCom3.yaml +++ b/kb/communities/Tomato_Oxylipin_SynCom3.yaml @@ -73,3 +73,49 @@ environmental_factors: description: Botrytis cinerea foliar infection and tomato oxylipin pathway perturbation. evidence: - *id001 +related_ingredients: +- preferred_term: oxylipin + chebi_term: + id: CHEBI:61121 + label: oxylipin + relevance: Oxylipins are the central class of plant defense signaling lipids that this + SynCom is designed to steer; the simplified community significantly intensified oxylipin + pathway activation in phytopathogen-infected leaves. + evidence: + - reference: PMID:37549573 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the activation of oxylipin pathways in the phytopathogen-infected leaves was + significantly intensified by the simplified community + explanation: Directly names oxylipin pathways as the defense response intensified by + this community. +- preferred_term: colneleic acid + chebi_term: + id: CHEBI:60956 + label: colneleic acid + relevance: Colneleic acid is one of the antimicrobial divinyl ethers whose biosynthesis + is required for the community-induced disease resistance; blocking its production + abolished protection against Botrytis cinerea. + evidence: + - reference: PMID:37549573 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic + and colnelenic acid, fully abolished the community-induced plant disease resistance + explanation: Names colneleic acid as an antimicrobial divinyl ether essential to the + community's disease resistance. +- preferred_term: colnelenic acid + chebi_term: + id: CHEBI:60959 + label: colnelenic acid + relevance: Colnelenic acid is the second antimicrobial divinyl ether downstream of the + oxylipin pathway whose loss abolishes community-induced resistance, marking it a key + protective metabolite of this SynCom. + evidence: + - reference: PMID:37549573 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic + and colnelenic acid, fully abolished the community-induced plant disease resistance + explanation: Names colnelenic acid as an antimicrobial divinyl ether essential to the + community's disease resistance.