Implications for personalised nutrition: Differential gut microbiota responses and substrate preferences during fibre-protein co-fermentation

Abstract

Vegan, omnivore, and protein-based diets each exert distinct effects on human physiology. This study examined the in vitro fermentation of dietary fibres: pectin (Pec), sugarcane fibre (Sgrc), and cassava-resistant starch (CassRS) and dietary proteins (pea, casein, and collagen), both individually and in combination, using faecal samples from a healthy volunteer. Gas production, short-chain fatty acid profiles, and microbiota composition were assessed. Results demonstrated clear interaction patterns depending on substrates. Additive effects were observed with PeaCassRS and CollagenCassRS, producing significantly more gas than either substrate alone, alongside increased butyrate (p < .0001). Neutral interactions were characterised by nonsignificant differences compared to isolated sample fermentation. Incorporating pectin demonstrated a negating effect by attenuating the fermentation of the mixed substrates. Substrate preferences were also evident: pectin outcompeted proteins, collagen was preferred over sugarcane fibre, while sugarcane fibre, CassRS, pea protein, and casein protein showed comparable fermentation rates. Microbial shifts were substrate dependent, with Bacteroides spp. dominating during protein fermentation and Lactobacillus spp. and Blautia spp. prevailing with pectin. Notably, Parabacteroides spp. increased significantly (p < .05) only when proteins were combined with CassRS. Showing that combining specific fibres and proteins can modulate gut microbiota and metabolites, opening new avenues for targeted nutritional therapeutics.