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.