Spatially Specialized Nasopharynx–Rectal Microbiomes in Golden Snub-Nosed Monkeys (Rhinopithecus roxellana)

Abstract

Simple Summary The golden snub-nosed monkey is an endangered primate, and understanding the microbes that live in different parts of its body could help us protect both the species and the broader ecosystems it inhabits. In this study, we compared the microbial communities living in the nasopharynx and rectum of these monkeys using full-length 16S rRNA amplicon sequencing and metagenomic analysis. We found that the two body sites host clearly different microbial communities. Functionally, the nasopharynx microbiome was enriched in pathways for breaking down certain amino acids and for antioxidant (glutathione) defense, while the gut microbiome specialized in processing sugars and building proteins. Notably, we detected relatively high levels of potentially disease-causing bacteria in the nasopharynx, including Helicobacter pylori and Chlamydia psittaci. These findings suggest that the nasopharynx and rectum represent distinct microbial environments in this endangered primate and highlight the nasopharynx as a possible reservoir of zoonotic pathogens, although larger studies are needed to confirm these patterns.