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Bound rumen enrichment graph to selection and measured phenotype #1767

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@realmarcin

Rumen_Substrate_Adapted_Lignocellulose_Enrichment_Consortia.yaml (CommunityMech:000389; PMID42197533): three substrate-enrichment observations are typed NICHE_PARTITIONING, but the four separately selected lines do not demonstrate reduced competition through within-community niche separation. Preserve all three positive composition/CMC/caproate observations and the existing enrichment-to-phenotype direction as PARTIAL. Genus abundance and caproate endpoints do not resolve member-to-member flux, a necessary mediator, hydrogen redistribution or methane reduction. Existing discussions already acknowledge hydrogen/methane and amplicon-scope limitations; preserve them. Complete fresh main text through Conclusions read. No new topology.

Dedup: fresh all-state issue titles/bodies and ignored/hidden-inclusive local search with .git/docs/site/references_cache excluded; relevant caches separately inspected. Matching issues read, not duplicates of these findings. Comments/PRs not exhaustive. Source-based self-adversarial review, not independent approval. Graph-repair issues close only after protected-main merge.

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  1. realmarcin commented on Oct 7, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1771 at c33f689; exact-head self-review: #1771 (review). 880 passed in 285.17s (0:04:45); postcommit docs-current passed.43 final validation outputs/digests plus decisions and provenance are committed. Four records changed;14nodes6existingdirections retained. The surviving SF356 pairwise-target finding was corrected with an additional append-only history and complete validation rerun;23 preliminary outputs retained. Non-graph1770 and existing loader1703/Linux DOI-cache1091 remain unresolved. Not independent approval; close only after protected-main merge.

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