You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
{{ message }}
Repository navigation
Separate minority-member label exchange, growth mediation and competition claims #1331
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.
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.
Activity
realmarcin commentedon Oct 6, 2026
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.