Gut Microbiome Shift of Japanese Macaques as a Result of Human Encroachment

Abstract

On a global scale, urban development is the fastest growing form of land use and has led to more severe human-wildlife conflict in recent years. Noting the role of gut microbiome in host physiology like nutrition and immune system, it is thus essential to understand how human-wildlife conflict can affect animals’ gut microbiome. This study therefore set out to assess the anthropogenic influence on gut microbiome of Japanese macaques and the possibility of using gut microbiome as indicator for anthropogenic influence. Using 16S rRNA gene sequencing, we described the microbiome composition of Japanese macaques Macaca fuscata experiencing different human disturbance levels - captive, provisioned, crop-raiding and wild. For alpha diversity, our result showed that observed richness of gut microbiome did not differ significantly between disturbance levels but between collection sites. For beta diversity, captive populations harbored the most distinctive gut microbiome composition, and had greatest difference with wild populations. Whereas for provisioned and crop-raiding groups, the macaques exhibited intermediate microbiome between wild and captive. Bacterial taxa from phyla Firmicutes, Bacteroidetes and Cyanobacteria demonstrated shift in abundance along the disturbance level. Specifically, we found Firmicutes to Bacteroidetes ratio and Cyanobacteria abundance elevated in wild macaques. In summary, this study revealed the flexibility of gut microbiome of Japanese macaques and the possibility of using gut microbiome profile in assessing the anthropogenic effect to non-human primates.