The Human Microbiome Project has improved our understanding of microbial and functional diversity. Lloyd-Price, Mahurkar et al. now report an expanded data set from the study, comprising 1,631 new metagenomes (2,355 total) from diverse body sites at multiple time points in 265 individuals. Strain-level metagenomic profiles revealed body site-specific subspecies clades and the authors were able to quantify species with phylogenetic diversity that were under-represented in isolate genomes. Moreover, species-level taxonomic profiling revealed co-occurrence patterns between bacterial species and several archaea, eukaryotes and viruses. Using functional profiling methods, the authors classified metabolic core pathways into universal, microbiome-enriched and body site-enriched; the latter being indicative of functional adaptation by the microbiota to a particular niche. Finally, the authors characterized microbial and functional variation over time at different body sites.