Chiang Edna, Deblois Courtney L, Carey Hannah V, Suen Garret
Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Anim Microbiome. 2022 Jan 3;4(1):1. doi: 10.1186/s42523-021-00154-9.
Hibernating 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.
Wild 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.
This 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.
冬眠动物经历饮食的极端变化，这使其成为理解宿主 - 微生物共生关系的有用系统。然而，我们目前关于冬眠动物肠道微生物群的大多数知识来自对圈养动物的研究。鉴于圈养环境和野生环境之间存在显著差异，从圈养冬眠动物研究得出的结论可能无法反映肠道微生物群在野生动物生理学中的作用。为了解决这个问题，我们使用基于Illumina的16S rRNA基因测序来比较夏季圈养和野生的13条纹地松鼠（TLGS）的盲肠细菌微生物群。作为第一项使用基于Illumina技术全年比较专性啮齿动物冬眠动物微生物群的研究，我们还报告了圈养TLGS微生物群在夏季、冬季和春季的变化。
与圈养微生物群相比，野生TLGS微生物群具有更高的丰富度和系统发育多样性，且β多样性的变化较小。被鉴定为核心操作分类单元（OTU）并发现对β多样性差异有显著贡献的分类群主要存在于毛螺菌科和瘤胃球菌科。圈养TLGS微生物群全年共享门和核心OTU，但活跃季节（夏季和春季）的微生物群与冬季微生物群具有不同的α和β多样性。
这是第一项比较圈养和野生啮齿动物冬眠动物微生物群的研究。我们的研究结果表明，由于圈养和野生地松鼠的微生物群不同，应分别解释它们的数据。此外，作为第一项使用基于Illumina的16S rRNA测序比较专性啮齿动物冬眠动物季节性微生物群的研究，我们报告的圈养TLGS微生物群变化与先前的研究一致。综上所述，本研究为提高未来冬眠微生物群研究的可重复性和实验设计提供了基础信息。
