Temporal variation of the microbiome is dependent on body region in a wild mammal (Tamiasciurus hudsonicus)

Microbial communities are increasingly being recognized as important to host health in wild mammals, but how these communities are characterized can have important consequences on the results of these studies. Previous research has explored temporal variation in microbial communities in humans and lab mammals, but few have investigated how microbiomes fluctuate in wild populations and none have examined the temporal dynamics of these fluctuations in different body regions on a wild mammal. Using Illumina MiSeq sequencing of the V3-V4 16S rRNA gene regions, we characterized the buccal and gut microbiomes of wild North American red squirrels, Tamiasciurus hudsonicus, to measure changes in these two microbiomes over short (<2 weeks), medium (2-4 weeks) and long (>1 month) term sampling periods. While we observed short and medium temporal stability in the buccal microbiome, the gut microbiome varied between medium and long-term sampling periods. There was no evidence of intra-individual correlations between buccal and gut microbiome change, suggesting that temporal stability is dependent on the body region and factors affecting microbial stability may be specific to body sites. From these findings, we urge researchers to be cautious in interpreting results from single temporal sampling periods when quantifying characteristic microbiomes in wild mammals.