The cecal microbial community's response to hibernation of thirteen-lined ground squirrels

Abstract

The presence of microbial communities within the gastrointestinal tract is extremely important. Intestinal associated microbial populations established immediately after birth and the population is maintained by diet. Hibernation is an adaptation that some animals use, during which an animal does not consume additional food. Due to this change in diet, a significant change in the intestinal microbiota is expected. Cecal material was collected from thirteen-lined ground squirrels at various stages relative to hibernation: pre-hibernation, inter-bout arousal, two hours post arousal, twenty-four hours post arousal, and seven days post arousal. Each cecal sample was used for community analysis via DNA extraction and sequencing of 16S rRNA genes and used to determine abundance via flow cytometry. Community analysis identified a progression where microbial communities prior to hibernation were dominated by phylum Firmicutes but during hibernation the community was dominated by Bacteroidetes. Each progressive stage post arousal from hibernation showed an increase in Firmicutes relative to Bacteroidetes culminating in a similar community structure at seven days post arousal to that seen pre-hibernation. Abundance followed a cycle starting with high abundance pre-hibernation followed by a significant reduction during inter-bout arousal. Abundance gradually restored at each stage post-arousal culminating in equivalent abundance to pre-hibernation.