ABSTRACTInteractions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Despite a recent proliferation of research on interactions between animals and their associated bacterial communities, comparative evidence from fungal communities is lacking, especially in natural populations. This disparity means knowledge of host-microbe interactions is biased towards the bacterial microbiome. Using samples from 49 species from eight metazoan classes, we demonstrate that the ecological distance between both fungal and bacterial components of the microbiome shift in tandem with host phylogenetic distance. Though so-called phylosymbiosis has been shown in bacterial communities, we extend previous knowledge by demonstrating that the magnitude of shifts in fungal and bacterial community structure across host phylogeny are correlated. These data are indicative of coordinated recruitment by hosts for specific suites of microbes, and potentially selection for bacterial-fungal interactions across a broad taxonomic range of host species. Using co-occurrence networks comprising both microbial groups, we illustrate that fungi form a critical component of microbial interaction networks, and that the strength and frequency of such interactions vary across host taxonomic groups. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.

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.