Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates

Abstract

The study of the mammalian microbiome serves as a critical tool for understanding host-microbial diversity and coevolution and the impact of bacterial communities on host health. While studies of specific microbial systems (e.g., in the human gut) have rapidly increased, large knowledge gaps remain, hindering our understanding of the determinants and levels of variation in microbiomes across multiple body sites and host species. Here, we compare microbiome community compositions from eight distinct body sites among 17 phylogenetically diverse species of nonhuman primates (NHPs), representing the largest comparative study of microbial diversity across primate host species and body sites. Analysis of 898 samples predominantly acquired in the wild demonstrated that oral microbiomes were unique in their clustering, with distinctive divergence from all other body site microbiomes. In contrast, all other body site microbiomes clustered principally by host species and differentiated by body site within host species. These results highlight two key findings: (i) the oral microbiome is unique compared to all other body site microbiomes and conserved among diverse nonhuman primates, despite their considerable dietary and phylogenetic differences, and (ii) assessments of the determinants of host-microbial diversity are relative to the level of the comparison (i.e., intra-/inter-body site, -host species, and -individual), emphasizing the need for broader comparative microbial analyses across diverse hosts to further elucidate host-microbial dynamics, evolutionary and biological patterns of variation, and implications for human-microbial coevolution. IMPORTANCE The microbiome is critical to host health and disease, but much remains unknown about the determinants, levels, and evolution of host-microbial diversity. The relationship between hosts and their associated microbes is complex. Most studies to date have focused on the gut microbiome; however, large gaps remain in our understanding of host-microbial diversity, coevolution, and levels of variation in microbiomes across multiple body sites and host species. To better understand the patterns of variation and evolutionary context of host-microbial communities, we conducted one of the largest comparative studies to date, which indicated that the oral microbiome was distinct from the microbiomes of all other body sites and convergent across host species, suggesting conserved niche specialization within the Primates order. We also show the importance of host species differences in shaping the microbiome within specific body sites. This large, comparative study contributes valuable information on key patterns of variation among hosts and body sites, with implications for understanding host-microbial dynamics and human-microbial coevolution.

Keywords: microbiome; nonhuman primates; variation.

FIG 1

(A) Relative abundances (%) of phylum-level microbial community compositions of different body sites for all host species combined. (B) Alpha (within-sample) diversity showing the species richness and evenness of all samples. Boxplots of observed ASVs (a qualitative measure of community richness) and Shannon’s diversity index (a quantitative measure of community richness). Results marked with the same letter are not statistically significantly different at an alpha value of 0.05, while results with different letters are statistically significantly different at an alpha value of 0.05. (C and D) Beta (between-sample) diversity, showing the distribution of samples. (C) PCoA plot of unweighted UniFrac distances (a qualitative measure of community dissimilarity that incorporates phylogenetic relationships between the microbial species). (D) PCoA plot of weighted UniFrac distances (a quantitative measure of community dissimilarity that incorporates phylogenetic relationships between the features).

FIG 2

(A and B) Beta (between-sample) diversity, showing the distribution of samples, for samples from all species contributing oral samples and samples from at least one other body site. (A) PCoA plot of unweighted UniFrac distance (a qualitative measure of community dissimilarity that incorporates phylogenetic relationships between the microbial species). (B) Boxplot of quantified interindividual distances within all body sites. Results marked with the same letter are not significantly different at an alpha value of 0.05, while results with different letters are significantly different at an alpha value of 0.05. (C and D) Oral, rectal, and penile/vaginal samples from chimpanzee, Verreaux’s sifaka, mangabey, and titi monkey. (C) Beta (between-sample) diversity, showing the distribution of samples. PCoA plot of unweighted UniFrac distances (a qualitative measure of community dissimilarity that incorporates phylogenetic relationships between the microbial species). (D) Boxplot of the quantified beta diversity distances within and between groups. (E) Rectal, penile, and vaginal samples from chimpanzee, Verreaux’s sifaka, mangabey, and titi monkey. Beta (between-sample) diversity, showing the distribution of samples. PCoA plot of unweighted UniFrac distances (a qualitative measure of community dissimilarity that incorporates phylogenetic relationships between the microbial species).

FIG 3

Oral, rectal, penile, and vaginal samples from chimpanzees, Verreaux’s sifakas, mangabeys, and titi monkeys. (A) Phylum-level microbial community compositions of samples. (B) Alpha (within-sample) diversity, showing the species richness and evenness of samples. Boxplots of observed ASVs (a qualitative measure of community richness) and Shannon’s diversity index (a quantitative measure of community richness). Results marked with the same letter are not significantly different at an alpha value of 0.05, while results with different letters are significantly different at an alpha value of 0.05. (C to F) Beta (between-sample) diversity, showing the distribution of samples. PCoA plots of unweighted UniFrac distances (a qualitative measure of community dissimilarity that incorporates phylogenetic relationships between the microbial species) for chimpanzee (C), titi monkey (D), Verreaux’s sifaka (E), and mangabey (F).