This study explores the co-evolution of mammals and their gut microbiota by analyzing the fecal microbiota of 106 mammals from 60 species across 13 taxonomic orders. The research reveals that host diet and phylogeny significantly influence bacterial diversity, with diversity increasing from carnivory to omnivory to herbivory. Bacterial communities co-diversify with their hosts, and human gut microbiota is typical of omnivorous primates. The study uses network-based analyses to map microbial community composition and structure onto mammalian phylogeny and diet, showing that same-species hosts have more similar microbial communities than different species. Diet clustering is highly significant, with herbivores, omnivores, and carnivores clustering separately. Stable isotope analysis confirms that diet influences microbial community composition, with carnivores having higher isotope values than herbivores. The study also shows that gut morphology affects microbial community composition, with foregut and hindgut fermenters clustering separately. The results suggest that gut microbiota have evolved to adapt to different diets, with herbivores having more diverse microbial communities. The study highlights the importance of diet and host phylogeny in shaping the gut microbiota, and suggests that the immune system's tolerance to gut microbes is a basal trait in mammal evolution. The findings provide insights into the co-evolution of mammals and their gut microbiota, and have implications for understanding human health and disease.This study explores the co-evolution of mammals and their gut microbiota by analyzing the fecal microbiota of 106 mammals from 60 species across 13 taxonomic orders. The research reveals that host diet and phylogeny significantly influence bacterial diversity, with diversity increasing from carnivory to omnivory to herbivory. Bacterial communities co-diversify with their hosts, and human gut microbiota is typical of omnivorous primates. The study uses network-based analyses to map microbial community composition and structure onto mammalian phylogeny and diet, showing that same-species hosts have more similar microbial communities than different species. Diet clustering is highly significant, with herbivores, omnivores, and carnivores clustering separately. Stable isotope analysis confirms that diet influences microbial community composition, with carnivores having higher isotope values than herbivores. The study also shows that gut morphology affects microbial community composition, with foregut and hindgut fermenters clustering separately. The results suggest that gut microbiota have evolved to adapt to different diets, with herbivores having more diverse microbial communities. The study highlights the importance of diet and host phylogeny in shaping the gut microbiota, and suggests that the immune system's tolerance to gut microbes is a basal trait in mammal evolution. The findings provide insights into the co-evolution of mammals and their gut microbiota, and have implications for understanding human health and disease.