Fecal Metabolic and Microbial Responses to Five Acute Fueling Strategies During a 60-Minute Rowing Protocol: A Randomized Crossover Multi-Omics Pilot Study

Background/Objectives: We compared next-morning fecal metabolic and microbial responses to five acute fueling strategies. Methods: Eight male recreational rowers with complete specimens from 12 crossover completers received an erythritol comparator, two carbohydrate doses, fixed carbohydrate–protein, and personalized carbohydrate–protein (P-CPS). Eighty specimens yielded 40 paired changes. Participant-blocked, period-adjusted models used restricted permutations and Benjamini–Hochberg false discovery rate (FDR) correction. Results: No primary global test passed across-modality FDR correction: SCFAs, p = 0.0321, q = 0.0963; metabolome, q = 0.1334; microbiome, q = 0.2813. No metabolite or originally annotated genus passed its omnibus FDR family. Post hoc SILVA 138.2 reclassification retained a nonsignificant global result but identified three low-count genus-level omnibus signals. Secondary change-score contrasts indicated higher isovaleric and isobutyric post/pre fold changes under P-CPS, fixed carbohydrate–protein, and high carbohydrate than under the comparator. However, no concentration or composite-endpoint contrast remained FDR-positive in post hoc models adjusting for same-trial pre-trial values. Caproic acid evidence also weakened with expanded correction and analytical-range checks. Two metabolome–SCFA principal-component correlations survived FDR correction and persisted after exclusion of overlapping annotations. Conclusions: This pilot identified model-sensitive secondary chemical signals without FDR-supported global intervention effects. Baseline imbalance, unmeasured beverage osmolality and fecal water, and quantification limitations preclude attributing these signals to increased fermentation or nutritional benefit.