Vertebrates harbor microbes both internally and externally, and collectively these microorganisms (the “microbiome”) contain genes that outnumber the host’s genetic information ten-fold. The majority of the microorganisms associated with vertebrates are found within the gut; where they influence host physiology, immunity, and development. The development of next generation sequencing has led to a surge in effort to characterize the microbiomes of various vertebrate hosts, a necessary first step to determine the functional role these communities play in host evolution or ecology. This shift away from a culture-based microbiological approach, limited in taxonomic breadth, has resulted in the emergence of patterns suggesting a core vertebrate microbiome dominated by members of the bacterial phyla Bacteroidetes, Proteobacteria and Firmicutes. Still, there is substantial variation in the methodology used to characterize the microbiome, from differences in sample type to issues of sampling captive or wild hosts; and the majority (>90%) of studies have characterized the microbiome of mammals, which represent just 8% of described vertebrate species. Here, we review the state of microbiome studies of non-mammalian vertebrates and provide a synthesis of emerging patterns in the microbiome of those organisms. We highlight the importance of collection methods, and the need for greater taxonomic sampling of natural rather than captive hosts; a shift in approach that is needed to draw ecologically and evolutionarily relevant inferences. Finally, we recommend future directions for vertebrate microbiome research, so that attempts can be made to determine the role that microbial communities play in vertebrate biology and evolution. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.