Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities

Abstract

Background: Host-associated microbes comprise an integral part of animal digestive systems and these interactions have a long evolutionary history. It has been hypothesized that the gastrointestinal microbiome of humans and other non-human primates may have played significant roles in host evolution by facilitating a range of dietary adaptations. We have undertaken a comparative sequencing survey of the gastrointestinal microbiomes of several non-human primate species, with the goal of better understanding how these microbiomes relate to the evolution of non-human primate diversity. Here we present a comparative analysis of gastrointestinal microbial communities from three different species of Old World wild monkeys.

Methodology/principal findings: We analyzed fecal samples from three different wild non-human primate species (black-and-white colobus [Colubus guereza], red colobus [Piliocolobus tephrosceles], and red-tailed guenon [Cercopithecus ascanius]). Three samples from each species were subjected to small subunit rRNA tag pyrosequencing. Firmicutes comprised the vast majority of the phyla in each sample. Other phyla represented were Bacterioidetes, Proteobacteria, Spirochaetes, Actinobacteria, Verrucomicrobia, Lentisphaerae, Tenericutes, Planctomycetes, Fibrobacateres, and TM7. Bray-Curtis similarity analysis of these microbiomes indicated that microbial community composition within the same primate species are more similar to each other than to those of different primate species. Comparison of fecal microbiota from non-human primates with microbiota of human stool samples obtained in previous studies revealed that the gut microbiota of these primates are distinct and reflect host phylogeny.

Conclusion/significance: Our analysis provides evidence that the fecal microbiomes of wild primates co-vary with their hosts, and that this is manifested in higher intraspecies similarity among wild primate species, perhaps reflecting species specificity of the microbiome in addition to dietary influences. These results contribute to the limited body of primate microbiome studies and provide a framework for comparative microbiome analysis between human and non-human primates as well as a comparative evolutionary understanding of the human microbiome.

Figure 1. Relative abundance of phylum members of fecal bacteria from nine wild primate subjects.

Ribosomal Database Project classifier (v.10.2; 70% confidence threshold) was used for sequence assignment. Sequence abundance from fecal samples of black-and-white colobus subjects are green; red colobus subjects are red; red-tailed guenon subjects are blue, and unclassified bacteria abundance are represented by grey color bars. The analysis is based on 534R dataset.

Figure 2. Heatmap display of the relative abundance of genera.

(534R dataset). The color spectrum represents abundance of each genus per thousand sequences; dark blue representing minimum relative abundance and dark red representing maximum relative abundance. The genera are shown in alphabetical order. Each subject is shown at the bottom of the figure; BW1-BW3: Black and white colobus subjects; RC1-RC3; Red colobus subjects, and RTG1-RTG3: Red-tailed guenon subjects.

Figure 3. Multi Dimensional Scale analysis of the microbiomes based on the 534R dataset.

non-metric Multi Dimensional Scale analysis is an ordination method used to visually assess variation in patterns of microbial diversity. Each data point represents 16S rRNA data from a single primate subject; Black and white colobus subjects, red-colobus subjects, and red-tailed guenon subjects are designated by symbols in green, red, and blue colors, respectively. The Bray-Curtis similarity was used to rank the distances calculated using the community data.

Figure 4. Multi Dimensional Scale analysis of the microbiomes based on the 27F dataset.

Each data point represents 16S rRNA data from a single primate subject; Black and white colobus subjects, red-colobus subjects, and red-tailed guenon subjects are designated by symbols in green, red, and blue colors, respectively. The Bray-Curtis similarity was used to rank the distances calculated using the community data.

Figure 5. Multi Dimensional Scale analysis of the microbiomes based on the (27F-534R) dataset.

Black and white colobus subjects, red-colobus subjects, and red-tailed guenon subjects are designated by symbols in green, red, and blue colors, respectively. The Bray-Curtis similarity was used to rank the distances calculated using the community data.

Figure 6. Multi Dimensional Scale analysis of the microbiomes based on the enriched (27F-534R) dataset.

The analysis was based on the (27F-534R) dataset, which include human stool data. Human subjects (A, B, C) were previously described elsewhere . Black and white colobus subjects, red-colobus subjects, red-tailed guenon subjects, and human subjects are designated by symbols in green, orange, blue, and purple colors, respectively. The Bray-Curtis similarity was used to rank the distances calculated using the community data.