Metagenomic insights into effect of pulse cell wall integrity on gut microbiota, CAZyme gene responses and starch/protein metabolism during in vitro fecal fermentation

The physical structure of pulse cotyledon cells modulates gut microbiota by controlling starch and protein availability for colonic fermentation, yet the mechanisms governing the interplay between saccharolytic and proteolytic fermentation remain unclear. Here, enzymatically treated white kidney bean cotyledon cells with weakened cell walls (CWs) underwent in vitro fecal fermentations and shotgun sequencing. Impaired CWs enhanced fermentation, increased acetate and propionate production, and reduced branched-chain fatty acids (BCFAs) and ammonia. Damaged CWs upregulated CAZymes encoding genes GH4, GH15, GH126, CBM20, and CBM26, which are associated with amylase, α-glucosidases, and amyloglucosidase activities involved in starch degradation. Furthermore, amino acid pathway enrichment revealed that IhgO and csiD, involved in lysine degradation, as well as astA-E, PRODH, putA and E1.2.1.88, involved in the conversion of arginine and proline to glutamate, were upregulated. Instead, isolated protein showed the highest ammonia and BCFAs production, accompanied by elevated glutamate dehydrogenase (gudB, GLUD1_2, and E1.4.1.4), soxA and soxB, involved in serine metabolism, and DBT, involved in branched-chain amino acid degradation. These findings provide metagenomic insights into how pulse CW integrity regulates saccharolytic and proteolytic fermentation, deepening our understanding of whole pulse foods in supporting gut health.