Cecal content and mucosa microbiotas of wild and captive (summer, torpor, interbout arousal, and spring) 13-lined ground squirrels

Hibernating animals naturally experience extreme changes in diet that make them fascinating systems in which to study host-microbe symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals and older 454 pyrosequencing technology. Differences between captive and wild environments and between sequencing technologies can impact microbiota results. To address these knowledge gaps, we used Illumina-based sequencing of the 16S rRNA gene to: (1) compare the bacterial gut microbiotas of wild and captive 13-lined ground squirrels (TLGS), and (2) compare Illumina-based sequencing of the TLGS microbiota across the hibernation cycle with previous 454 pyrosequencing results.