Species‐level exploration of the gut microbiome in the leaf‐eating Presbytis monkeys reflected the effects of anthropogenic activity and specialized dietary niches: Conservation on the fourth biodiversity level

Abstract Seventy‐five percent of nonhuman primates have declining populations caused by deforestation and habitat loss, mainly due to human disturbance worldwide. Endangered white‐headed langurs and François' langurs are two allopatric species inhabiting limestone forests. Given the negative effects of human disturbance on the gut microbial community, we investigated the gut microbial composition and function in these two wild langurs under human disturbance (with the zoo as a reference for the strongest disturbance) using multiple methods (landscape, nutritional analysis, behavioral observation, 16S rRNA gene full‐length sequencing of 237 samples, and deep metagenomic sequencing). We found that the relative abundance of four typical human disturbance‐related (HDR) gut microbial families (Lachnospiraceae and Bacteroidaceae) increased with growing human disturbance. We identified the gut microbial species involved in the main dietary or host‐derived component digestion (e.g., diet‐derived polysaccharides, oxalate, and host‐derived glycans) based on a comparative genomic analysis of the non‐redundancy of 1199 metagenomic assembled genomes. These langurs harbored some putative common cellulolytic and oxalate‐degrading bacteria, and also harbored some host‐specific bacteria. Thus, we conclude that increased HDR species in the langur population might be caused by dietary changes and increased sugar intake, such as steamed bread of corn and sorghum, fruits in the zoo, and anthropogenic diet, corn, and sweet potatoes in wild langurs. Factors such as diet, host, and living environment under anthropogenic disturbance may influence the gut microbial community and function in these langurs. The langur gut microbiome plays a potential role in helping the host adapt to the leaf diet and limestone living environment. In the future, wild primate conservation should not only focus on host genetic diversity but also on the changes in symbiotic microbiomes under anthropogenic disturbance.