Researchers have uncovered critical relationships between gut microbiota-derived proteins and metabolic regulation, opening avenues for chronic disease therapies. Identification of bacterial proteins resembling muscle-derived hormones shows potential for appetite and blood sugar modulation. Complementary investigations synthesize extensive microbiome data across agri-food systems to highlight the integral role microbes play in health. In parallel, studies illuminate metabolic and mitochondrial dysfunction linked to neurodegenerative diseases such as Parkinson’s via epigenetic mechanisms.