Extended Data Figure 1: Extended body-wide metagenomic taxonomic profiles in HMP1-II.

a, The combined HMP1-II datasets include a total of 2,355 metagenomes (724 previously published and 1,631 new, including 252 technical replicates). These span the project’s six targeted body sites (anterior nares, buccal mucosa, supragingival plaque, tongue dorsum, stool, and posterior fornix) in addition to at least 20 samples each from 3 additional sites, of the 18 total sampled sites: retroauricular crease, palatine tonsils, and subgingival plaque. Metagenomes are now available for at least one body site for a total of 265 individuals. b, PCoA using Bray–Curtis distances among all microbes at the species level. c, Relative abundances of the most prevalent and abundant microbes (bacterial, viral, eukaryotic, and archaeal) among all body sites, as profiled by MetaPhlAn2²⁰. Prevalent eukaryotic microbes are shown at the genus level. d, Taxonomic profiles do not vary more between sequencing centres, batches, or clinical centres than they do among individuals within body sites. Ordinations show Bray–Curtis principal coordinates of species-level abundances at each body site. Within-site ecological structure is as expected¹, with no divergence associated with technical variables along the first two ordination axes.