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Separate minority-member label exchange, growth mediation and competition claims #1331

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Description

@realmarcin

Finding

Source-based self-adversarial review of CommunityMech:000333 against the full primary main body finds three overstatements:

  • Calcein/mCherry exchange is not identified metabolite cross-feeding or proof that a physical shuttle causes the growth benefit. Filtered N. vulgaris/E. coli supernatant also improves C. acetobutylicum growth without simultaneous contact with that recipient.
  • The paper's passive-competition wording does not establish this repository's COMPETITION (-/-) type: early E. coli growth appears unaffected. pH, glucose depletion, metabolites and filtered supernatants do not reproduce every live-coculture feature.
  • The inhibition-to-protection arrow restates the phenotype being attenuated, not an upstream cause. Faster second-phase OD600 growth is not itself a colonization or establishment assay.

Acceptance

Retain the observed label exchange, proposed shuttle, directed inhibition, supported E. coli-associated lactate uptake and N. vulgaris addition/supernatant effects. Remove both unsupported arrows and categorical transfer/competition/colonization types where the assays do not support their exact definitions. Distinguish mixed-culture growth-phase estimates from taxon-specific live-cell doubling; genomic qPCR is copies per ng DNA with extraction limitations. Add a focused gap, history, ledger, tests and generated page. Do not add structure.

Read the whole record and full Introduction, Results, Discussion, Methods, seven main figure captions; not images/supplements. Exact-record/PMID/DOI search over 669 issue titles/bodies found only #746, an existing GTDB reproducibility followup. Read #746, #749, #752, #1316 and #1317; broader enum and different-pair findings are not duplicates. Local searches included ignored/hidden files. Comments not exhaustive.

Activity

  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Addressed in #1334 at cf322d4f9793d1a7e6ebd14eabefca78bf805fdb. Exact-head source-based self-adversarial review: #1334 (review). All 30 local gates and actual post-commit docs-current passed; 254 passed in 157.48s (0:02:37); 75 MATCH snippets, zero other classes; 3 passed in 1.54s; 48 unrelated raw blocks and five caches byte-preserved. See committed batch20 decision/adversarial/validation records for assay bounds and full node/arrow accounting. This issue remains open until protected main merge; #1333 is separate non-graph work.

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