Altered microbiota diversity in captive NHPs relative to wild conspecific NHPs
We tested for effects of host species identity and captivity state on microbiota alpha and beta diversity using 16S rDNA sequences from captive chimpanzee samples generated by the present study (Captive chimpanzees USA2) and published data from humans (Humans), wild chimpanzees (Wild chimpanzees TZA; Wild chimpanzees DRC), and captive and wild red-shanked doucs (Captive douc SGP, Captive douc USA, Wild douc VNM). Captive populations tended to display reduced Shannon entropy relative to wild conspecifics (Figure S2; Table S2). However, results from Chao1 analyses were mixed, with captive doucs displaying lower alpha diversity than wild conspecifics but captive chimpanzees and gorillas displaying higher alpha diversity than wild conspecifics (Figure S2; Table S2).
Analyses of beta diversity indicated that the gut microbiotas of captive primate populations were compositionally distinct from the gut microbiotas of wild conspecifics (PERMANOVA p -value = 0.001 in each comparison). This distinctiveness of captive and wild NHP gut microbiotas was evident in principal coordinates analyses based on Sorensen-Dice distances (Figure 1A). Moreover, for each NHP species the gut microbiotas of captive populations were significantly more similar to those of humans than were the gut microbiotas of wild-living conspecific populations (Figure 1B) (Monte-Carlo nonparametric permutation tests p -value = 0.001). The relative abundances of ASVs for each sample are presented in Table S3. The relative abundances of microbial genera for each sample are presented in Table S4.