Separate prebiotic SynCom intervention effects from direct pairwise transfer and donor-community claims #1512

Record: kb/communities/Infant_Gut_Prebiotic_Response_SynCom.yaml (000281).

The network-to-hub arrow describes a broad finding identifying one of its components rather than an established causal direction. The P.vulgatus/E.coli node is typed as direct pairwise cross-feeding, whereas the primary preprint reports a controlled community-omission effect on E.coli metabolic activity underGOS; conditioned supernatants did not reproduce the condition difference. Succinate/propionate production and the activity effect are distinct measurements, not evidence of a specified direct donor-to-recipient transfer.

The primary preprint is version1,2026-05-29. Its six-member SynCom and donor-derived cultures are different experiments; donor P.dorei/L.rhamnosus must not be treated as SynCom P.vulgatus/L.gasseri. Preserve the positive omission, isotope/Raman-FISH, acid-challenge and substrate-response results. Bound the lactate-versus-acetate effects and proposed community mediation; do not invent a pH-clamped challenge protocol. The main text discusses additive pH/acid effects, while the exact challenge protocol is not specified in its main Methods and supplements have not been inspected.

Complete freshly retrieved primary XML main text, Methods and embedded Figures1-5 captions read. No original images, supplementary files, raw data or code audited. Repair existing nodes/arrows with explicit experimental contexts and supported canonical subsets. Exact roster and missing source-backed representation are a separate unresolved follow-up. Keep this repair open until protected-main merge.

Dedup:817 all-state issues and43 ignored/hidden local matches. #1425/#1428 and#1259/#1262 concern different HMO systems; #292/#293 concern another record's B.ovatus identifier, not this finding.