From aldabra giant tortoises to humans: how diet and age influence gut microbiota structure and function across vertebrates

The gut microbiota plays a crucial role in host physiology by metabolizing dietary carbohydrates via carbohydrate-active enzymes (CAZymes) and producing short-chain fatty acids (SCFAs). This research explores microbiome dynamics across vertebrates, integrating studies on tortoises and humans. First, in Aldabra giant tortoises, wild populations harbor greater microbial diversity than captive individuals. Infant tortoises exhibit higher CAZyme gene diversity, particularly from Bacteroides cellulosilyticus, suggesting enhanced carbohydrate metabolism early in life. Second, a human dietary fiber intervention shows rapid increases in SCFA levels, particularly acetate and propionate, alongside delayed enrichment of Parabacteroides, a CAZyme-rich genus. Third, a comparative analysis of 35 vertebrate species reveals widespread conservation of CAZyme families and SCFA-producing taxa across reptiles, birds, and mammals, despite differences in host diet and phylogeny. These findings highlight the interplay between diet, age, and microbial function, demonstrating that while microbiome composition varies, core metabolic pathways remain evolutionarily conserved.