The diversity of microbes within a given body habitat can be defined as the number and abundance distribution of distinct types of organisms, which has been linked to several human diseases: low diversity in the gut to obesity and inflammatory bowel disease2,3, for example, and high diversity in the vagina to bacterial vaginosis4. For this large study involving microbiome samples collected from healthy volunteers at two distinct geographic locations in the United States, we have defined the microbial communities at each body habitat, encountering 81–99% of predicted genera and saturating the range of overall community configurations (Fig. 1, Supplementary Fig. 1 and Supplementary Table 1; see also Fig. 4). Oral and stool communities were especially diverse in terms of community membership, expanding prior observations5, and vaginal sites harboured particularly simple communities (Fig. 1a). This study established that these patterns of alpha diversity (within samples) differed markedly from comparisons between samples from the same habitat among subjects (beta diversity, Fig. 1b). For example, the saliva had among the highest median alpha diversities of operational taxonomic units (OTUs, roughly species level classification, see http://hmpdacc.org/HMQCP), but one of the lowest beta diversities—so although each individual’s saliva was ecologically rich, members of the population shared similar organisms. Conversely, the antecubital fossae (skin) had the highest beta diversity but were intermediate in alpha diversity. The vagina had the lowest alpha diversity, with quite low beta diversity at the genus level but very high among OTUs due to the presence of distinct Lactobacillus spp. (Fig. 1b). The primary patterns of variation in community structure followed the major body habitat groups (oral, skin, gut and vaginal), defining as a result the complete range of population-wide between-subject variation in human microbiome habitats (Fig. 1c). Within-subject variation over time was consistently lower than between-subject variation, both in organismal composition and in metabolic function (Fig. 1d). The uniqueness of each individual’s microbial community thus seems to be stable over time (relative to the population as a whole), which may be another feature of the human microbiome specifically associated with health.

Figure 1: Diversity of the human microbiome is concordant among measures, unique to each individual, and strongly determined by microbial habitat. a, Alpha diversity within subjects by body habitat, grouped by area, as measured using the relative inverse Simpson index of genus-level phylotypes (cyan), 16S rRNA gene OTUs (blue), shotgun metagenomic reads matched to reference genomes (orange), functional modules (dark orange), and enzyme families (yellow). The mouth generally shows high within-subject diversity and the vagina low diversity, with other habitats intermediate; variation among individuals often exceeds variation among body habitats. b, Bray–Curtis beta diversity among subjects by body habitat, colours as for a. Skin differs most between subjects, with oral habitats and vaginal genera more stable. Although alpha- and beta-diversity are not directly comparable, changes in structure among communities (a) occupy a wider dynamic range than do changes within communities among individuals (b). c, Principal coordinates plot showing variation among samples demonstrates that primary clustering is by body area, with the oral, gastrointestinal, skin and urogenital habitats separate; the nares habitat bridges oral and skin habitats. d, Repeated samples from the same subject (blue) are more similar than microbiomes from different subjects (red). Technical replicates (grey) are in turn more similar; these patterns are consistent for all body habitats and for both phylogenetic and metabolic community composition. See previously described sample counts1 for all comparisons. PowerPoint slide Full size image

No taxa were observed to be universally present among all body habitats and individuals at the sequencing depth employed here, unlike several pathways (Fig. 2 and Supplementary Fig. 2, see below), although several clades demonstrated broad prevalence and relatively abundant carriage patterns6,7. Instead, as suggested by individually focused studies2,3,5,8,9, each body habitat in almost every subject was characterized by one or a few signature taxa making up the plurality of the community (Fig. 3). Signature clades at the genus level formed on average anywhere from 17% to 84% of their respective body habitats, completely absent in some communities (0% at this level of detection) and representing the entire population (100%) in others. Notably, less dominant taxa were also highly personalized, both among individuals and body habitats; in the oral cavity, for example, most habitats are dominated by Streptococcus, but these are followed in abundance by Haemophilus in the buccal mucosa, Actinomyces in the supragingival plaque, and Prevotella in the immediately adjacent (but low oxygen) subgingival plaque10.

Figure 2: Carriage of microbial taxa varies while metabolic pathways remain stable within a healthy population. a, b, Vertical bars represent microbiome samples by body habitat in the seven locations with both shotgun and 16S data; bars indicate relative abundances colored by microbial phyla from binned OTUs (a) and metabolic modules (b). Legend indicates most abundant phyla/pathways by average within one or more body habitats; RC, retroauricular crease. A plurality of most communities’ memberships consists of a single dominant phylum (and often genus; see Supplementary Fig. 2), but this is universal neither to all body habitats nor to all individuals. Conversely, most metabolic pathways are evenly distributed and prevalent across both individuals and body habitats. PowerPoint slide Full size image

Figure 3: Abundant taxa in the human microbiome that have been metagenomically and taxonomically well defined in the HMP population. a–c, Prevalence (intensity, colour denoting phylum/class) and abundance when present (size) of clades in the healthy microbiome. The most abundant metagenomically-identified species (a), 16S-identified genera (b) and PATRIC12 pathogens (metagenomic) (c) are shown. d, e, The population size and sequencing depths of the HMP have well defined the microbiome at all assayed body sites, as assessed by saturation of added community metabolic configurations (rarefaction of minimum Bray–Curtis beta-diversity of metagenomic enzyme class abundances to nearest neighbour, inter-quartile range over 100 samples) (d) and phylogenetic configurations (minimum 16S OTU weighted UniFrac distance to nearest neighbour) (e). PowerPoint slide Full size image

Additional taxonomic detail of the human microbiome was provided by identifying unique marker sequences in metagenomic data11 (Fig. 3a) to complement 16S profiling (Fig. 3b). These two profiles were typically in close agreement (Supplementary Fig. 3), with the former in some cases offering more specific information on members of signature genera differentially present within habitats (for example, vaginal Prevotella amnii and gut Prevotella copri) or among individuals (for example, vaginal Lactobacillus spp.) One application of this specificity was to confirm the absence of NIAID (National Institute of Allergy and Infectious Diseases) class A–C pathogens above 0.1% abundance (aside from Staphylococcus aureus and Escherichia coli) from the healthy microbiome, but the near-ubiquity and broad distribution of opportunistic ‘pathogens’ as defined by PATRIC12. Canonical pathogens including Vibrio cholerae, Mycobacterium avium, Campylobacter jejuni and Salmonella enterica were not detected at this level of sensitivity. Helicobacter pylori was found in only two stool samples, both at <0.01%, and E. coli was present at >0.1% abundance in 15% of stool microbiomes (>0% abundance in 61%). Similar species-level observations were obtained for a small subset of stool samples with 454 pyrosequencing metagenomics data using PhylOTU13,14. In total 56 of 327 PATRIC pathogens were detected in the healthy microbiome (at >1% prevalence of >0.1% abundance, Supplementary Table 2), all opportunistic and, strikingly, typically prevalent both among hosts and habitats. The latter is in contrast to many of the most abundant signature taxa, which were usually more habitat-specific and variable among hosts (Fig. 3a, b). This overall absence of particularly detrimental microbes supports the hypothesis that even given this cohort’s high diversity, the microbiota tend to occupy a range of configurations in health distinct from many of the disease perturbations studied to date3,15.