Yeast-Mediated Pre-Fermentation Modulates the Fecal Microbiome In Vitro in a Genotype-Dependent Manner

This study investigated the effects of yeast-mediated pre-fermentation on the composition and functional characteristics of modern and ancient wheat genotypes, and their subsequent impact on gut microbial fermentation. Whole wheat flours were pre-fermented using Saccharomyces cerevisiae (6%, w/w) at 30 °C for 6 h. Raw and pre-fermented whole wheat samples were subjected to in vitro upper gastrointestinal digestion, followed by monosaccharide composition analysis, in vitro fecal fermentation using a pooled inoculum prepared from three healthy donors, microbial profiling, and short-chain fatty acid (SCFA) quantification. Fermentation increased Folin–Ciocalteu-reactive values and antioxidant capacity, while reducing residual starch and protein after digestion, indicating alterations in the composition of digestion-derived residues. After fermentation by S. cerevisiae, monosaccharide analysis revealed a relative enrichment of glucose, accompanied by decreased proportions of arabinose and xylose. Following in vitro fecal fermentation, pre-fermented wheat samples exhibited significantly (p < 0.001, AMOVA) different microbial community structures compared with their raw counterparts, based on Bray–Curtis dissimilarities, whereas differences in α-diversity were comparatively limited. In addition, taxa associated with carbohydrate fermentation and SCFA production, including Parabacteroides distasonis, Butyrivibrio crossotus, and Kineothrix, showed treatment- and genotype-dependent responses. All wheat samples supported SCFA production, although SCFA accumulation was more gradual than with inulin. Overall, yeast-mediated pre-fermentation was associated with changes in wheat composition and subsequent shifts in fecal microbial community structure and fermentation dynamics, with responses varying among wheat genotypes.