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Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
Published on: March 19, 2018
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Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing
Edna Chiang1, Courtney L Deblois1, Hannah V Carey2
1Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Animal Microbiome
|January 4, 2022
Summary
Wild hibernator gut microbiotas are more diverse than captive ones. Captive and wild ground squirrel data should be analyzed separately due to distinct gut microbial communities.
Area of Science:
- Microbiology
- Animal Physiology
- Ecology
Background:
- Hibernating animals offer insights into host-microbial symbioses due to extreme dietary shifts.
- Existing research on hibernator gut microbiota primarily uses captive animals, potentially misrepresenting wild physiology.
- Substantial environmental differences exist between captive and wild settings for hibernating species.
Purpose of the Study:
- To compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) during summer.
- To investigate seasonal changes in the gut microbiota of captive TLGS.
- To establish foundational data for future hibernation microbiota studies.
Main Methods:
- Illumina-based sequencing of the 16S rRNA gene was employed.
- Bacterial cecal microbiotas of captive and wild TLGS were analyzed.
- Seasonal microbiota changes in captive TLGS (summer, winter, spring) were assessed.
Main Results:
- Wild TLGS microbiotas exhibited greater richness and phylogenetic diversity than captive ones.
- Core operational taxonomic units (OTUs) contributing to beta diversity differences were mainly from Lachnospiraceae and Ruminococcaceae families.
- Captive TLGS showed distinct alpha and beta diversities between active (summer/spring) and winter seasons.
Conclusions:
- Captive and wild ground squirrel microbiotas are distinct, necessitating separate interpretation of data.
- Seasonal variations in captive TLGS microbiota align with previous research.
- This study provides crucial baseline data for improving future hibernation microbiota research design and reproducibility.
