Wire M-P coculture GEM paper into Methylomicrobium-Chlorella community#63
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…ella doi:10.20517/mrr.2023.70 (Badr/He/Wang 2023, "Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling") is an orphan cache that develops three genome-scale modeling approaches - SteadyCom, dynamic FBA Lab, and their new DynamiCom - on a methanotroph-photoautotroph (M-P) coculture model system. Wire it as PARTIAL evidence on the Methane-and-Carbon-Dioxide-Mitigation cross-feeding interaction in the existing Methylomicrobium-Chlorella community: same kind of methanotroph-microalga consortium as the curated record, and the abstract directly speaks to "the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture" - which is the central claim of that interaction. PARTIAL because the modeled M-P system in the paper is generic rather than the specific M. alcaliphilum 20Z + Chlorella HS2 pairing curated here. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR adds a new publication (doi:10.20517/mrr.2023.70) as PARTIAL, COMPUTATIONAL evidence to the existing Methylomicrobium–Chlorella Methane Sequestration Coculture community, aiming to support the “Methane and Carbon Dioxide Mitigation” cross-feeding interaction using genome-scale modeling results from a related (generic) methanotroph–photoautotroph coculture system.
Changes:
- Adds a new evidence item referencing doi:10.20517/mrr.2023.70 under the “Methane and Carbon Dioxide Mitigation” interaction.
- Introduces a multi-fragment abstract snippet (using
..) and an explanation describing the paper’s modeling-based support as partial.
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- Move the GEM-modeling evidence off the Methane-and-Carbon-Dioxide-
Mitigation interaction and onto Saline-Metabolic-Coupling-and-pH-
Recovery. The paper's central claims are about metabolic coupling
driving enhanced coculture growth, not CH4/CO2 mitigation or
biomass carbon sequestration; the new placement aligns the
evidence with what the snippet actually supports ("robust
metabolic coupling between the two microbes" is the lead evidence
on this interaction).
- Author/year correction: "Badr/He/Wang 2023" -> "Badr/He/Wang 2024"
to match the journal's 2024-05-27 publication date in Crossref
(the "2023" in the DOI path 10.20517/mrr.2023.70 is the
volume/issue stamp, not the publication year).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This was referenced May 17, 2026
realmarcin
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May 18, 2026
* Regenerate community HTML and UMAP Refresh docs/ to reflect community additions and evidence updates since the last regen (PR #54). UMAP grows from 252 -> 261 embedded communities; 7 existing community pages are refreshed with the evidence additions from PRs #55, #58, #60, #61, #62, #63, #66, #67; 9 new community pages are added (2 from this session: Alaska Tundra Permafrost Iron-Redox and Saccharomyces-Acinetobacter Lignocellulose Detox; 7 from other curation work merged in between). - gen-html: 264 community pages rendered without error - gen-umap: 261 communities embedded (3 host-only skipped because none of their taxa have NCBITaxon embeddings) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Address Copilot review on PR #71: render evidence everywhere it lives Three template/data fixes triggered by the Copilot review on the HTML/UMAP regen: - src/communitymech/templates/community.html: - Extend the interaction-network color map and legend with PREDATION, NICHE_PARTITIONING, STRAIN_COMPETITION, and COLONIZATION_FACILITATION. Previously these enum values fell back to generic gray on the force-directed graph and were omitted from the legend, making 5+ community pages (Cellulomonas-Rhodobacter, Sphingobium-Rhodococcus, Clostridium-Carboxidivorans-Kluyveri, Rhodopseudomonas- Geobacter-Magnetite, plus any others) hard to read. - Render evidence on taxonomy entries via an "evidence-row" span. The previous template only rendered evidence inside ecological_interactions and growth_media, so evidence wired onto taxon blocks in PRs like #61 and #62 was on-disk in the YAML but invisible in the rendered HTML. - Render evidence on environmental_factors with the same expanding-row pattern. This is where PR #62 wired the Ter Horst 2021 peat-virome evidence on the SPRUCE community; it now appears in the HTML. - Add an "External Resources" section (analogous to Associated Datasets) that renders external_resources entries including their per-resource evidence. This is where PR #66 wired the Smith 2025 BioModels reproducibility paper on the Kefir BioModels community; it now appears in the HTML. - kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml: add `metals_present: [IRON]`, `metal_relevance: SIGNIFICANT`, and metal_notes describing the Fe(III) reduction / Fe(II) oxidation cycle this community is built around. The community was previously absent from the iron/metal index filter despite being entirely iron-centric. - docs/: regenerate all 264 community pages with the new template + the Alaska_Tundra metals metadata. Many pages pick up the new evidence-row block; the four pages with NICHE_PARTITIONING interactions now render those nodes with the dedicated color and include the new legend entries. Verified after regen: - SPRUCE community page now shows PMID:38515239 and PMID:34836550 (zero matches before, two each after). - Kefir BioModels community page now shows PMID:41343683 (zero matches before, two after). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
`doi:10.20517/mrr.2023.70` (Badr/He/Wang 2023, Microbiome Research Reports, "Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling") is an orphan cache that develops three GEM approaches — SteadyCom, dynamic FBA Lab, and the authors' new `DynamiCom` — on a methanotroph-photoautotroph (M-P) coculture model system.
Wire as PARTIAL evidence on the Methane and Carbon Dioxide Mitigation cross-feeding interaction in the existing `Methylomicrobium-Chlorella Methane Sequestration Coculture` community:
PARTIAL because the modeled M-P system in the paper is generic, not the specific M. alcaliphilum 20Z + Chlorella HS2 pairing curated here.
Test plan
🤖 Generated with Claude Code