The Human Microbiome Project (HMP) has characterized the microbial communities of healthy individuals, revealing significant diversity and specialization in various body habitats such as the gut, skin, and vagina. The study analyzed 4,788 specimens from 242 adults, finding that microbial communities vary widely among individuals, with strong niche specialization. The project identified 81–99% of the genera and community configurations present in the Western microbiome, and observed stable metabolic pathways despite variation in community structure. Ethnic/racial background was a strong predictor of both pathways and microbes. The study highlights the range of structural and functional configurations of the healthy human microbiome, providing insights into its epidemiology, ecology, and translational applications. Inter-individual variation in microbial carriage was observed at the species and strain levels, with some taxa being universally absent across all body habitats and individuals. The microbiome's response to physical factors, host immunological factors, and microbial interactions was also studied, showing that microbial community structure can vary discontinuously or continuously. The study concludes that the human microbiome's uniqueness even in a reference population underscores the need for prospective within-subjects designs in future studies.The Human Microbiome Project (HMP) has characterized the microbial communities of healthy individuals, revealing significant diversity and specialization in various body habitats such as the gut, skin, and vagina. The study analyzed 4,788 specimens from 242 adults, finding that microbial communities vary widely among individuals, with strong niche specialization. The project identified 81–99% of the genera and community configurations present in the Western microbiome, and observed stable metabolic pathways despite variation in community structure. Ethnic/racial background was a strong predictor of both pathways and microbes. The study highlights the range of structural and functional configurations of the healthy human microbiome, providing insights into its epidemiology, ecology, and translational applications. Inter-individual variation in microbial carriage was observed at the species and strain levels, with some taxa being universally absent across all body habitats and individuals. The microbiome's response to physical factors, host immunological factors, and microbial interactions was also studied, showing that microbial community structure can vary discontinuously or continuously. The study concludes that the human microbiome's uniqueness even in a reference population underscores the need for prospective within-subjects designs in future studies.