Beyond nutrition: How single-cell proteins reshape the gut microbiota and metabolome

Single-cell proteins (SCPs), protein-rich biomass from yeasts, filamentous fungi, microalgae, and bacteria, have undergone rapid commercial expansion: over 35 products are now globally available, scientific publications and patent filings have grown substantially over the past decade, and global protein demand is projected to increase by at least 50% by 2050. Regulatory evaluation remains limited to amino acid scores, digestibility, and nucleic acid safety, overlooking the distinct cell wall matrices each SCP class delivers to the colon as fermentation substrate. This review synthesizes in vitro, animal, and human evidence on how the four SCP classes modulate gut microbiota and the colonic metabolome through their cell wall polysaccharides and nitrogenous residues. The gut microbiota-metabolome axis, encompassing SCFA production, bile acid remodeling, the tryptophan-indole pathway, and proteolytic catabolism, is the primary mediator that translates SCP structural properties into signals relevant to intestinal barrier integrity, immune homeostasis, and cardiometabolic health. SCP effects on gut microbiota and metabolome are source-specific and processing-dependent. Polysaccharide-rich SCPs promote saccharolytic fermentation and enrich butyrate-producing taxa (Roseburia spp., Faecalibacterium prausnitzii), while bacterial SCPs lacking colonic polysaccharide shift fermentation toward proteolytic catabolism. Microalgal SCPs, besides polysaccharides, deliver bioactive compounds, including phycocyanobilin and sulfated exopolysaccharides. Mycoprotein is the only SCP class with human clinical evidence of gut-mediated cardiometabolic effects, showing a 10% reduction in LDL-cholesterol and a 13% reduction in fasting blood glucose. Gut microbiota-metabolome endpoints must be integrated into SCP clinical trials to enable health claim substantiation and population-level dietary guidance.