Dataset Open Access

Primate phageomes are structured by superhost phylogeny and environment

Gogarten, Jan F.; Rühlemann, Malte; Archie, Elizabeth; Tung, Jenny; Akoua-Koffi, Chantal; Bang, Corinna; Deschner, Tobias; Muyembe-Tamfun, Jean-Jacques; Robbins, Martha M.; Schubert, Grit; Surbeck, Martin; Wittig, Roman M.; Zuberbühler, Klaus; Baines, John F.; Franke, Andre; Leendertz, Fabian H.; Calvignac-Spencer, Sébastien

Zenodo Dataset 1. Contigs. Contigs generated for each sample that were >500bp in length.

Zenodo Dataset 2. Visualizations of phage phylogenies with tests for superhost-specificity (wild primates and humans). Phage phylogenies, with the superhost indicated by the color of the circles at the tip, as in Fig. 2A. Branches supported by SH-like aLRT values <0.95 are dashed. The P-values in the lower left corner of each phylogeny indicate the results of the test for whether within-superhost taxa distances were lower than between-superhost taxa distances [categorical Mantel test].

Zenodo Dataset 3. Baboon phage phylogenies. The superhost’s social group indicated by the color of the circles at the tip, as in Fig. 3A. Branches supported by Shimodaira-Hasegawa-like approximate likelihood ratio test values <0.95 are dashed. The P-values in the lower left corner of each phylogeny indicate the results of the comparison of the pairwise distance between sequences from group members and non-group members using a categorical Mantel test.

Zenodo Dataset 4. Phage phylogenies including sequences from captive and wild non-human primates, as well as those from humans. Tips are colored as in Fig. 3. Next to each phylogeny is a box plot of pairwise phage distances, after downsampling to one phage from each superhost taxon/location. The comparisons of phages from captive primates and wild primates, captive primates and humans, as well as between wild primates and humans are shown in these boxplots.

Zenodo Dataset 5. Mapping files of contigs >500bp for each sample mapped to the HHAP.

Zenodo Dataset 6. Manually trimmed mapped contigs (wild non-human primates and humans). Manually selected region conserved across many samples and taxa.

Zenodo Dataset 7. Maximum likelihood estimates of the phylogenies of 208 phages generated using alignment of conserved region (wild non-human primates and humans).

Zenodo Dataset 8. Manually trimmed mapped contigs of the complete dataset (captive and wild non-human primates and humans). Considered the same region as was selected for the wild primate and human dataset.

Zenodo Dataset 9. Maximum likelihood estimates of the phylogenies of 208 phages generated using alignment of conserved region (captive and wild non-human primates and humans).

Abstract: Humans harbor diverse communities of microorganisms, the majority of which are bacteria in the gastrointestinal tract. These gut bacterial communities in turn host diverse bacteriophage (hereafter phage) communities that have a major impact on their structure, function, and ultimately human health. However, the evolutionary and ecological origins of these human-associated phage communities are poorly understood. To address this question, we examined fecal phageomes of 23 wild non-human primate taxa, including multiple representatives of all the major primate radiations. We find relatives of the majority of human-associated phages in wild primates. Primate taxa have distinct phageome compositions that exhibit a clear phylosymbiotic signal, and phage-superhost co-divergence is often detected for individual phages. Within species, neighboring social groups harbor compositionally and evolutionarily distinct phageomes, which are structured by superhost social behavior. Captive non-human primate phageome composition is intermediate between that of their wild counterparts and humans. Phage phylogenies reveal replacement of wild great ape-associated phages with human-associated ones in captivity and surprisingly, show no signal for the persistence of wild-associated phages in captivity. Together, our results suggest that potentially labile primate-phage associations have persisted across millions of years of evolution. Across primates, these phylosymbiotic and sometimes co-diverging phage communities are shaped by transmission between groupmates through grooming and are dramatically modified when primates are moved into captivity.
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