Structural differences in prebiotic-resistant dextrins drive human gut microbiota and glycoside hydrolase profiles in ex vivo continuous fermentations

Prebiotics, mainly carbohydrates of dietary origin, modulate gut microbiota (GM) composition and function, being digested and fermented by resident fibrolytic and glycolytic microorganisms. However, the precise mechanisms by which the nature of prebiotics influences the gut microbiota in terms of diversity, richness and activity remain poorly understood, complicated by inter-individual variability. In this study, we investigated the effects of prebiotic-resistant glucans (RGs), with subtle biochemical differences - derived from two distinct production processes - on GM diversity, richness, and fibrolytic function. Using an ex vivo human colonic fermentation model combined with shotgun metagenomic sequencing, we obtained a precise picture of the microbial ecosystem, encompassing metagenomic species pangenomes (MSPs), glycoside hydrolase (GH) gene profiles, and short-chain fatty acid (SCFA) production. Our findings revealed that microbial consortia first evolved according to the donor's baseline microbiota, then in response to fibre type, forming specialized communities dominated by Bacteroidetes and Firmicutes. These consortia retained biodiversity while becoming enriched in fibrolytic species and predicted monosaccharidase genes targeting both ?- and ?-glycosidic linkages. Strong correlations between fibre type, MSP composition, and GH gene abundance indicated that RGs produced through the same process have close effects on GM. These results open new perspectives for the rational design of prebiotics aimed at selectively modulating gut microbiota, and optimizing their impact.