Our studies show clear differences in the cutaneous microbiota at a single reference site (forearm) between peoples in the United States and Amerindians in Venezuela. The similarities between the samples from the two US locations to one another in relation to the Amerindian samples (Supplemental Figure 1
), despite some differences in study methods, are consistent with prior US studies of the cutaneous microbiota that show conservation of the major taxa (Gao et al., 2007
; Grice et al., 2009
; Costello et al., 2009
). In contrast, the microbiota from the Amerindians was substantially different from the United States, and was divided into two major clusters that were essentially not represented in the US samples. The alpha diversity indices indicate relative similarities in species richness (and evenness) among persons differing substantially in both ethnicity and life style (United States and Cluster A); however, for a second group of Amerindian samples (Cluster B), there was much higher richness and evenness. Thus, Cluster B differed from both the United States and Cluster A, and the differences were apparent even at low sampling depth (100 sequences or sample; ).
Both the US sample and Cluster A were dominated by a single major taxon, but which differed from one another (Propionibacterium
in the US sample, and Staphylococcus
in Cluster A), whereas in Cluster B, there was no single dominant taxon. These observations bear some resemblance to other human body sites, for example, the enterotypes described in the intestinal microbiome (Arumugan et al., 2011
), or the different major patterns observed in the vagina (Zhou et al., 2010
), in that there are clusters with continuous variation linking the clusters. However, in these latter cases, the major types are present in all geographic groups studied, whereas Cluster B was found essentially only in the Amerindians. However, sampling of other populations will be needed to determine the diversity of clustering patterns.
An alternative possibility is that the populations clustered are not fixed, but could change from one predominant type into the other, such as has been sometimes observed in longitudinal studies of the vaginal microbiota (Ravel et al., 2011
). Nevertheless, although the US sample and Cluster A have a dominant taxon, the differences between the three groups (US, Cluster A, and Cluster B) extend to taxa that have intermediate or rare representation (). Thus, at this single point of sampling, the patterns are robust. This also is shown by the UniFrac analysis of the pairwise distances, in which the inter-group distances always are greater than the intra-group distances. These findings indicate that on average, when the entire microbial community is taken into account (rather than just the first few principal components), individuals from the same group are more similar than individuals in different groups.
Platanillal, the village sampled is representative of a population in transition; two to three generations ago its peoples were nomadic hunter-gatherers (Steward and Faron, 1959
; Salzano and Callegari-Jacques, 1988
), but now the peoples are settled in permanent homes, with access to aspects of modern life, yet with a still relatively traditional diet. Reflecting a lack of piped water, carriage of intestinal protozoa and helminths is universal (Supplemental Table 1
), and multiple species is the rule. Nevertheless, although the hypothesis that carriage of parasites (helminths and protozoa) changes immunological balance (for example, in a Th2 direction) (Maizels et al., 2009
; Fyhrquist et al., 2012
), which could then affect microbiota composition, is attractive, we did not find support for this idea, and we could not identify a factor that distinguished between carriage of a Cluster-A or Cluster-B cutaneotype. There was no association with age, gender, body mass index, relation to bathing, drinking water, or use of soap, or parasite type or overall burden and individuals differing in type often lived in the same household. Further sampling and longitudinal studies will be needed to discern the important correlates.
Finally, there is intensive interest in variation of the human microbiome in relation to health and disease (Peterson et al., 2009
; Qin et al., 2010
). However, many of the constituents of the microbiota have deep ancestral relationships with their hosts (Linz et al., 2007
; Ley et al., 2008
). Modernization is changing our microecology (Blaser, 2006
; Dethlefsen et al., 2008
; Blaser and Falkow, 2009
). To understand the composition and function of the human microbiome before the development of processes associated with postmodern life, we should seek and sample indigenous people before they become more subject to modernization, which is rapidly advancing around the world. By sampling more groups of individuals in varied locales who have retained more traditional lifestyles, we may be better able to discover more extensive variation in the cutaneous microbiota.