Separate gut proteome overlap from demonstrated niche and yield mechanisms #1503

Source-based self-adversarial finding

kb/communities/Human_Gut_FourMember_Proteome_Complementarity_Consortium.yaml, PMID:42032280, three nodes and two arrows.

The graph treats partner effects as excluding carbon-source effects, annotated KO overlap as demonstrated competitive niche partitioning, and higher community productivity as mutual benefit. Metabolite lists overstate measured exchange. The study explicitly did not directly measure competition or coexistence, and its overlap/productivity association does not establish selective mediation.

Resolution

Preserve the positive co-culture proteomic findings and the abundance-matched mixed-isolate controls. Bound expression/KO overlap and the productivity association to the measured outcomes, with explicit four-member canonical participants. Both carbon and partners can affect proteomes. Do not project pooled human/rumen results onto every human condition or member. Preserve the Methods productivity denominator (mean monoculture qPCR abundance), not a sum or best-monoculture benchmark. Remove unsupported interaction types, qualify arrows and add exact-node gaps and regressions.

Complete cached primary main text, Methods and embedded main/extended-data captions read; no original figure images, supplementary files, raw data or code audited. No new causal structure is required for these repairs. Self-adversarial review is not independent approval. Keep open until protected-main merge.