Long-term natural studies are valuable for examining the effects of host demographics and environmental factors on animal microbiomes, and how those effects interact and shift over time. We examined how the cloacal microbiome of Sceloporus virgatus (the striped plateau lizard) varies under natural conditions in southeastern Arizona, USA, in a multi-year study. Cloacal swabs were collected from wild-caught lizards across their entire active season over three years. Analyses of 16S rRNA data generated on the Illumina platform revealed cloacal microbiomes of S. virgatus vary as a function of sex, season, size, and reproductive state, and do so independently of one another. Briefly, microbial diversity was higher in females than in males, increased with body size, was lowest in both sexes during the reproductive season, and was lowest in females when they were vitellogenic. It was not significantly affected by hibernation. This study highlights the importance of long term, wide scale microbiome studies for capturing accurate perspectives on microbiome diversity and composition in a given species. It also serves as a warning for comparisons of microbiomes across species, as each may be under a different suite of selective pressures from external or innate factors, which may differ in a species-specific manner.

Sequences of the 16s V4 regions were generated at IBest Genomics Core (University of Idaho) on the Illumina MiSeq platform. Detailed methodology can be found in Bunker et al., 2022, Wild microbiomes of striped plateau lizards vary with sex, body size, and reproductive season (2022), or in the attached README file.