This paper explores the evolution of the vertebrate gut microbiota, comparing bacterial assemblages associated with humans, other mammals, and free-living microbial communities. The human gut microbiota is influenced by diet, host morphology, and phylogeny, and is typical for an omnivorous primate. However, it is highly differentiated from free-living communities not associated with animal body habitats. The authors suggest that the recently initiated Human Microbiome Project should include a broad representation of humans, other mammals, and environmental samples to explore the evolutionary history of the biosphere. They also discuss the impact of diet on human evolution, the role of the adaptive immune system in shaping gut microbiota, and the potential for co-diversification between host and microbial lineages. The paper emphasizes the urgency of sampling microbial diversity due to rapid global changes and biodiversity loss.This paper explores the evolution of the vertebrate gut microbiota, comparing bacterial assemblages associated with humans, other mammals, and free-living microbial communities. The human gut microbiota is influenced by diet, host morphology, and phylogeny, and is typical for an omnivorous primate. However, it is highly differentiated from free-living communities not associated with animal body habitats. The authors suggest that the recently initiated Human Microbiome Project should include a broad representation of humans, other mammals, and environmental samples to explore the evolutionary history of the biosphere. They also discuss the impact of diet on human evolution, the role of the adaptive immune system in shaping gut microbiota, and the potential for co-diversification between host and microbial lineages. The paper emphasizes the urgency of sampling microbial diversity due to rapid global changes and biodiversity loss.