Gut microbiota plays an important role in health and metabolism and is affected by diet. This means that the gut microbiota of sympatric species is different due to niche separation. In this study, high-throughput 16S rRNA sequencing was used to study the gut microbiota of sympatric Francois’ langurs and rhesus macaques using 57 fecal samples collected from the limestone forests of the Guangxi Chongzuo White-headed Langur National Nature Reserve. The results indicated no significant difference in gut microbial diversity between the two primate species. However, marked differences were found in gut microbial composition. Francois’ langurs had a greater abundance of Firmicutes, Verrucomicrobia, TM7, and Planctomycetes, and a lower abundance of Bacteroidetes, Tenericutes, Proteobacteria, WPS-2, Fibrobacteres, and Lentisphaerae than rhesus macaques. At the genus level, Francois’ langurs had a greater abundance of norank Ruminococcaceae, unclassified Clostridiales, norank Clostridiales, Akkermansia, and unclassified Ruminococcaceae, whereas macaques had a higher proportion of Prevotella, Coprococcus, and Oscillospira. Predictive functional analysis reveals that the gut microbiota of Francois’ langurs is richer in cellular processes pathways than that of rhesus macaques, which were richer in genetic information processing and organismal systems. In summary, significant differences in gut microbiota were evident between the two sympatric primate species, which is probably due to the diet separation and morphology of the digestive tract. This suggests niche separation between the sympatric limestone-dwelling rhesus macaques and Francois’ langurs.
