Protective role of the vulture facial and gut microbiomes aid adaptation to scavenging

Background Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial and gut microbiomes from the black and turkey vultures. We characterized i ) the functional potential and taxonomic diversity of their microbiomes, ii ) the potential pathogenic challenges they face, and iii) elements in the microbiome that could play a protective role to the vulture’s face and gut. Results We found elements involved in diseases, such as periodontitis and pneumonia (more abundant in the face), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing health beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasites and antiinsectisides in the face. Based on the identified phages, we suggest that phages aid in the control, and possibly elimination as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we also identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role though biofilm formation played by Fusobacteria and Clostridia in the gut. Conclusions Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.