Fecal bacterial communities of wild black capuchin monkeys (Sapajus nigritus) from the Atlantic Forest biome in Southern Brazil are divergent from those of other non-human primates

•Identification of gut microbiota of Brazilian wild black capuchin monkeys.•Monkeys from two fragments of the Atlantic Forest biome in southern Brazil reveal specific gut bacterial communities.•In contrast to Firmicutes and Bacteroidetes predominant in non-human primate populations worldwide, Proteobacteria phylum was prevalent in Brazilian wild black capuchin monkeys.•Metabolic prediction revealed a microbiota associated with xenobiotics biodegradation, secondary metabolites and metabolism of terpenoids and polyketides pathways could positively affect monkey`s health and conservation facing anthropogenic environment. Gut microbiota are influenced by factors such as diet, habitat, and social contact, which directly affect the host's health. Studies related to gut microbiota in non-human primates are increasing worldwide. However, little remains known about the gut bacterial composition in wild Brazilian monkeys. Therefore, we studied the fecal microbiota composition of wild black capuchin monkey (Sapajus nigritus) (n=10) populations from two different Atlantic Forest biome fragments (five individuals per fragment) in south Brazil. The bacterial community was identified via the high-throughput sequencing and partial amplification of the 16S rRNA gene (V4 region) using an Ion Personal Genome Machine (PGMTM) System. In contrast to other studies involving monkey microbiota, which have generally reported the phyla Firmicutes and Bacteroidetes as predominant, black capuchin monkeys showed a high relative abundance of Proteobacteria (χ¯= 80.54%), followed by Firmicutes (χ¯= 12.14%), Actinobacteria (χ¯= 4.60%), and Bacteriodetes (χ¯= 1.31%). This observed particularity may have been influenced by anthropogenic actions related to the wild habitat and/or diet specific to the Brazilian biome's characteristics and/or monkey foraging behavior. Comparisons of species richness (Chao1) and diversity indices (Simpson and InvSimpson) showed no significant differences between the two groups of monkeys. Interestingly, PICRUSt2 analysis revealed that metabolic pathways present in the bacterial communities were associated with xenobiotic biodegradation and the biosynthesis of secondary metabolites, which may suggest positive effects on monkey health and conservation in this anthropogenic habitat. Infectious disease-associated microorganisms were also observed in the samples. The present study provides information about the bacterial population and metabolic functions present in