Gut Microbiome Composition of Wild and Captive Black Capuchin Monkeys (Sapajus nigritus)

The gut microbiome plays a key role in host physiology and is influenced by multiple factors, including environmental conditions. However, the effects of host environment on the gut microbiota of Neotropical primates remain poorly understood. This study compared the gut microbiomes of wild and captive black capuchin monkeys (Sapajus nigritus) from southern Brazil using 16S rRNA gene sequencing. Microbial diversity, community structure, differential taxonomic abundance, and predicted functional potential were assessed using multivariate analyses, DESeq2, Random Forest, and PICRUSt2. Host environment was significantly associated with gut bacterial community composition (PERMANOVA, p = 0.004), and captive individuals exhibited greater microbial richness. Wild monkeys were dominated by Pseudomonadota, particularly Enterobacteriaceae and Morganellaceae, with Proteus, Escherichia-Shigella, and Morganella as predominant genera. In contrast, captive monkeys showed higher relative abundances of Bacteroidota, especially Bacteroidaceae and Dysgonomonadaceae, with Bacteroides and Dysgonomonas among the predominant genera. Random Forest classification yielded an AUC of 0.934, although classification performance was lower for captive individuals. Predicted functional profiles differed between groups, with pathways related to amino acid biosynthesis, fatty acid β-oxidation, and mucin degradation enriched in wild monkeys, whereas pathways related to the degradation of aromatic and xenobiotic compounds were enriched in captive animals. Overall, these findings indicate that gut microbiome composition and predicted functional potential varied among black capuchin monkey populations, suggesting that specific factors associated with diet, environmental exposure, and husbandry conditions may contribute to microbiome variation.