Biodiversity of protists and nematodes in the wild nonhuman primate gut

Abstract

Documenting the natural diversity of eukaryotic organisms in the nonhuman primate (NHP) gut is important for understanding the evolution of the mammalian gut microbiome, its role in digestion, health and disease, and the consequences of anthropogenic change on primate biology and conservation. Despite the ecological significance of gut-associated eukaryotes, little is known about the factors that influence their assembly and diversity in mammals. In this study, we used an 18S rRNA gene fragment metabarcoding approach to assess the eukaryotic assemblage of 62 individuals representing 16 NHP species. We find that cercopithecoids, and especially the cercopithecines, have substantially higher alpha diversity than other NHP groups. Gut-associated protists and nematodes are widespread among NHPs, consistent with their ancient association with NHP hosts. However, we do not find a consistent signal of phylosymbiosis or host-species specificity. Rather, gut eukaryotes are only weakly structured by primate phylogeny with minimal signal from diet, in contrast to previous reports of NHP gut bacteria. The results of this study indicate that gut-associated eukaryotes offer different information than gut-associated bacteria and add to our understanding of the structure of the gut microbiome.

Fig. 1

Relative abundance of taxonomic groups document Fungi-dominated and Amoebozoa-dominated eukaryotic assemblages. Platyrrhines, most apes, and lemurs tend to be dominated primarily by Ascomycota, while cercopithecoids are dominated by Amoebozoa. Corresponding histograms illustrate the log transformed number of raw reads (gray bars) and log transformed reads after insects, vertebrates, and plants were removed (white bars), as well as the proportion of reads post filter that belong to known gut residents for each sample

Fig. 2

Diversity patterns of eukaryotes in the NHP gut microbiome. a Phylogeny of NHP species in this study. Shapes throughout figures correspond to NHP genus, color indicates NHP phylogroup. *No gorilla samples were included in diversity analyses because of low read counts. b PCoA of weighted UniFrac distances of the full eukaryotic assemblage. The majority of variance (69.75%) separates the cercopithecines and two apes from all other NHPs. The single Papio individual clustering away from the Papio group has the lowest overall proportion of Amoebozoa as compared with other members of its genus. c Higher alpha diversity in the eukaryotic assemblage is positively correlated with higher bacterial alpha diversity using a simple linear model (Pearson product moment correlation R = 0.44), a pattern that is also supported when host phylogeny is accounted for (p = 0.01)

Fig. 3

Phylotypes of Entamoeba display both host specificity and sharing across NHP groups. a Maximum likelihood tree of Entamoeba phylotypes with Entamoeba species and number of phylotypes indicated. Each dot represents a single NHP individual and color indicates NHP species. Each row of dots indicates a single phylotype corresponding to the phylogenetic tree. Lighter colored dots reflect samples in which an OTU was detected but at much lower relative abundance (below 0.001). Detection may therefore be an artifact of sequencing and should be interpreted with caution. b Bar chart summarizing the number of phylotypes found in each NHP species colored by NHP phylogroup. c Upset plot illustrating host-specificity of Entamoeba phylotypes. Unconnected dots indicate phylotypes found only in one NHP species. Connected dots indicate phylotypes that are shared between two or more NHP species. Numbers within dots indicate the number of shared phylotypes. Colors reflect NHP phylogroup

Fig. 4

Phylotype host-specificity among gut-resident nematode groups. a Maximum likelihood tree of nematode phylotypes that are probable gut residents with nematode group and number of phylotypes indicated. Each dot represents a single NHP individual and color indicates NHP species group. Each row of dots indicates a single phylotype corresponding to a tip in the phylogenetic tree. Lighter colored dots indicate very low abundance in a sample, as in Fig. 3. b Bar chart summarizing the number of nematode phylotypes found in each NHP species colored by NHP phylogroup. c Upset plot illustrating host-specificity of nematode phylotypes. Unconnected dots are phylotypes found in only one NHP species. Connected dots indicate phylotypes shared by two or more NHP species. Numbers within dots indicate the number of phylotypes

Fig. 5

High diversity of Iodamoeba sp. RL1 found in Pap. hamadryas, Pap. anubis, and C. ascanius. Statistical parsimony network of Iodamoeba phylotypes found in the current dataset. Size of node corresponds to the number of OTUs that are collapsed into the node after trimming positions in the alignment where there is a gap in at least 10% of all sequences. Number listed on branches indicates the number of stepwise mutations between nodes