For many species, one of the most important ecological relationships is between a host and the complex community of microbes associated with that host, commonly known as the microbiome. Some microbiomes are highly specialized to benefit their hosts, while others can be variable and dependent on environmental factors. One such specialized microbiome exists in the cloacae of Sceloporus virgatus, which is specialized for protection of eggs during incubation. In this study we examine the microbiome of three Sceloporus species using DNA from cloacal swabs, sequenced on the Illumina platform. We directly compare S. virgatus, an oviparous lizard found in riparian oak-pine woodlands in the southwestern United States to S. jarrovi, a species which shares habitat with S. virgatus but is viviparous. We then compared S. virgatus to a population S. occidentalis, another oviparous lizard that lives in similar habitat in more temperate regions of the western US. Then we compared three different populations of S. occidentalis that persist in different habitats – low elevation beach, low elevation forest, and the same high elevation riparian woodland population. Finally, we captured insects from all four habitats, to determine the contribution of diet to the microbiome. Results/Conclusions We found a distinct bifurcation of community phenotype from cloacal swabs of both S. virgatus and S. occidentalis, and show that higher diversity communities result from contamination by the animal’s own feces – a caution to other researchers using swab sampling. We were able to use Lachnospiraceae as a “feces-indicator” to limit further analyses to only uncontaminated samples. We found differences between the S. virgatus cloacal microbiome and both S. occidentalis and S. jarrovi microbiomes, although these dissimilarities manifest differently. S. occidentalis and S. virgatus, both oviparous, are dominated by Enterobacteriaceae, and the between-species variation is in low abundance taxa and at the ASV level; the viviparous S. jarrovi had less abundant Enterobacteriaceae and differed from S. virgatus in major taxa. There were also differences in the S. occidentalis microbiome between the three populations, with high elevation having much lower diversity. Only the S. occidentalis lizards from the low elevation forest showed any substantial overlap between the microbes present in the cloaca and the insect microbiome, but that overlap varied widely by individual. These results indicate that, while environmental effects can alter the microbiome, oviparous Sceloporus lizards may have a specialized core microbiome that is resilient, and determined by host evolution.
