Assessing the gut microbiome and the influence of host genetics on a critically endangered primate, the Northern muriqui (Brachyteles hypoxanthus)

Abstract

Abstract Background The Northern muriqui (Brachyteles hypoxanthus) is one of the world’s most critically endangered primates, currently represented by only ~ 1000 remaining mature individuals in the wild. The largest new world primate, this endemic herbivore plays an important role in seed dispersal in the Brazilian Atlantic Forest. However, due to several threats such as habitat loss and hunting, the species is in sharp decline and conservation actions are paramount to safeguarding its persistence. Analyses of gut microbiomes in wild populations can contribute to assessing the health status of the host species through the identification of microbial community changes which could lead to increased host vulnerability and disease. This can ultimately contribute to baseline knowledge towards improving conservation programmes and reintroduction efforts. Results In this study, we analysed the microbiome (using 16S rRNA metabarcoding) of faecal samples belonging to 53 uniquely genotyped individuals from three social groups located in a protected area (Caparaó National Park) aiming to provide the first assessment of the microbiome diversity and composition for this species. Our results showed the muriqui gut microbiome was predominantly composed of the phyla Bacteroidetes and Firmicutes, with the dominant classes represented by Bacteroidia and Clostridia. High similarity in both alpha and beta diversities was found for individuals from distinct groups, suggesting a lower environmental filtering effect on microbiota composition and a negligible geographical effect at the fine spatial scale analysed. Additionally, no significant effect of heterozygosity levels on microbiota diversity was recovered, but a significant influence of genetic distance on microbiota community structure and composition was demonstrated. Conclusions Here, we showed the importance of host genetics on the microbiome and highlighted that although the analysed populations are deemed isolated due to putative environmental barriers, they host a similar microbiome composition, with faecal microbiome stability possibly associated with host genetics, and the linked shared feeding strategies. Furthermore, the detailed wild Northern muriqui microbiome assessment herein included might be used for subsequent management and conservation actions considering future anthropogenic impact assessments on the species and animal relocations and/or reintroductions.