UFMP graph: distinguish hypothesized MAG roles and lactate transfer from measured fermentation #1474

CommunityMech:000029; GLBRC_UFMP_Fermentation_Community; PMID:37324413; doi:10.3389/fbioe.2023.1173656.

The complete cached primary main body, Methods, tables and captions explicitly describe a conceptual model of hypothesized roles. Reactor HPLC/GC-MS measures products; MAG pathways, abundance correlations, EtfB phylogeny and gene neighborhoods infer members and substrates. CLOS1 is proposed to elongate lactate predominantly to butyrate, LCO1 to elongate lactose directly, and ACID1 possibly ethanol (inconclusive). Do not imply all Firmicutes depend on Actinobacteriota-derived lactate, that ATO3-to-CLOS1 flux was traced, or that complete feedstock conversion or obligatory syntrophy was demonstrated. No terminal-chain-length genomic diagnostic was identified.

Acceptance: qualify all three existing nodes and both retained model arrows as HYPOTHESIZED/PARTIAL; retain the positive reactor measurements separately from COMPUTATIONAL member assignment; name exact canonical guild participants rather than representative pair endpoints; do not silently credit SPH2 to a lactate guild it does not belong to. Remove unjustified stereospecific CHEBI:422 assertions rather than guess a replacement. Preserve #486/#624 taxonomy work and all non-graph raw blocks. Add a focused flux/perturbation gap, guarded history, tests and hash-bound decision/validation records. No new causal structure or provider spend required.

Source-based self-adversarial review, not independent approval. All three whole YAML records were read. Main text, Methods and embedded captions were read; no figure images, separate supplementary files, raw data or analysis code audited. Dedup searched 790 all-state issue titles/bodies and ignored/hidden-inclusive reports, research, history, tests, scripts and workflows. Five matched issue bodies (#624/#543/#486/#326/#17) and the UFMP/Garlic prior history artifacts were read; none duplicates these source-specific causal-scope repairs. Existing validation and render logs also match record names but do not constitute completed source reviews. Not every issue comment or PR review was inspected.