Abstract
BackgroundHibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota’s role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring.ResultsWild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas.ConclusionsThis is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.
Highlights
Host-microbe symbioses are dynamic, especially in animals that experience extreme shifts in diet as these changes dramatically alter substrate availability for their gut microbiota
To our knowledge, the first analysis of Illumina-based sequencing from an obligate rodent hibernator across active and hibernation seasons, we reported changes in captive the 13-lined ground squirrel (TLGS) microbiotas across the year
We found that Wild microbiotas had greater richness and phylogenetic diversity and decreased variance in beta diversity compared to Captive microbiotas
Summary
Host-microbe symbioses are dynamic, especially in animals that experience extreme shifts in diet as these changes dramatically alter substrate availability for their gut microbiota. The winter hibernation season is characterized by cycling between periods of depressed and normal metabolism (torpor and interbout arousal, respectively). Due to fasting during hibernation, the gut microbiota is forced to rely solely on host-derived substrates (e.g., mucins) as its source of energy. The hibernation season ends with the emergence aboveground in spring and the resumption of normal metabolic activity and feeding patterns. This natural cycle of extreme changes in diet and physiology makes mammalian hibernators like the TLGS useful systems for studying host-microbe symbioses. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we reported changes in captive TLGS microbiotas in summer, winter, and spring
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