Bacterial community variation in human body habitats across space and time

Abstract

Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions. We found that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.

Fig. 1

16S rRNA gene surveys reveal hierarchical partitioning of human-associated bacterial diversity. (A to D) Communities clustered using PCoA of the unweighted UniFrac distance matrix. Each point corresponds to a sample colored by (A) body habitat, (B) host sex, (C) host individual, or (D) collection date. The same plot is shown in each panel. F, female; M, male. (E and F) Mean (± SEM) unweighted UniFrac distance between communities. In (E) habitats are weighted equally and in (F) skin comparisons are within sites. (G) UPGMA clustering of composite communities from the indicated locales. Leaves are colored according to body habitat as in (A). R, right; L, left.

Fig. 2

Site-to-site variation on skin surfaces. (A) Rarefaction curves for communities sampled from skin and other habitats. Phylogenetic diversity is in units of branch length. Mean ± 95% confidence interval shown. (B) PCoA plot as in Fig. 1 showing only dorsal tongue, forehead, and volar forearm samples. (C) Individual rarefaction curves for forehead and palm communities.

Fig. 3

Community assembly on forehead versus volar forearm skin surfaces. (Upper) Mean (± SEM) weighted UniFrac distance between communities. At each time point, P < 0.01 unless indicated; two-tailed t tests. ns, not significant. (Middle) Mean (± SEM) phylogenetic diversity controlled for sampling effort. (Bottom) Mean (± SEM) relative abundance of Propionibacterium spp.