Faecal Bacterial and Short-Chain Fatty Acid Profiles in Response to 48 h FODMAP Intervention Prior to Endurance Exercise

Background/Objectives: Short-term low-fermentable oligo-, di-, and monosaccharide and polyol (FODMAP) diets can reduce exercise-associated gastrointestinal symptoms (Ex-GIS); however, their effects on the gut microbiome, short-chain fatty acids (SCFAs), and gastrointestinal biomarkers remain unclear. This study explored the effects of 48 h dietary FODMAP manipulation within a high-carbohydrate diet on faecal bacterial and SCFA profiles, and their relationships with exercise-induced gastrointestinal syndrome (EIGS) biomarkers, Ex-GIS, and performance. Methods: Twelve endurance athletes experiencing Ex-GIS were randomly allocated to a 48 h high-carbohydrate (mean ± SD: 12.1 ± 1.8 g∙d⁻¹)–high-FODMAP (HC-HFOD) (54.8 ± 10.5 g∙d⁻¹) and a 48 h high-carbohydrate–low-FODMAP (HC-LFOD) (3.0 ± 0.2 g∙d⁻¹) diet before 2 h of running at 60% $\dot{V}$O_2max, followed by a 1 h distance test (22.9 ± 1.2 °C, 46 ± 8% RH). Baseline faecal samples were collected before exercise trials to determine faecal bacterial and SCFA profiles. Blood samples were collected pre- and post-exercise to determine plasma I-FABP, sCD14, and CRP concentrations. Ex-GIS were recorded every 15 min throughout exercise. Results: Faecal bacterial α-diversity and relative abundance (RA%) at the phylum level were unchanged following both diets, while several family- and genus-level taxa RA% values were changed (p < 0.05), with greater shifts after HC-HFOD. HC-HFOD significantly increased faecal total-SCFA (p = 0.004), acetic (p = 0.002), and butyric (p = 0.028) acid concentrations. Strong positive and negative correlations between bacterial RA% and EIGS biomarkers and Ex-GIS were observed. Strong negative correlations with bacterial RA% and performance were observed. Conclusions: The 48 h HC-HFOD resulted in greater increases in bacterial RA% and SCFA concentrations compared with baseline. Bacterial RA% correlated bidirectionally with EIGS biomarkers and Ex-GIS, alongside strong negative associations with performance.