Sharpton Thomas J, Stagaman Keaton, Sieler Michael J, Arnold Holly K, Davis Edward W
Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA.
Department of Statistics, Oregon State University, Corvallis, OR 97331, USA.
Toxics. 2021 Jan 15;9(1):10. doi: 10.3390/toxics9010010.
Zebrafish are increasingly used to study how environmental exposures impact vertebrate gut microbes. However, we understand little about which microbial taxa are common to the zebrafish gut across studies and facilities. Here, we define the zebrafish core gut microbiome to resolve microbiota that are both relatively robust to study or facility effects and likely to drive proper microbiome assembly and functioning due to their conservation. To do so, we integrated publicly available gut microbiome 16S gene sequence data from eight studies into a phylogeny and identified monophyletic clades of gut bacteria that are unexpectedly prevalent across individuals. Doing so revealed 585 core clades of bacteria in the zebrafish gut, including clades within , , , , , , , and . We then applied linear regression to discern which of these core clades are sensitive to an array of different environmental exposures. We found that 200 core clades were insensitive to any exposure we assessed, while 134 core clades were sensitive to more than two exposures. Overall, our analysis defines the zebrafish core gut microbiome and its sensitivity to exposure, which helps future studies to assess the robustness of their results and prioritize taxa for empirical assessments of how gut microbiota mediate the effects of exposure on the zebrafish host.
斑马鱼越来越多地被用于研究环境暴露如何影响脊椎动物的肠道微生物。然而，对于跨研究和实验设施的斑马鱼肠道中哪些微生物类群是常见的，我们了解甚少。在此，我们定义了斑马鱼核心肠道微生物群，以解析那些对研究或实验设施效应相对稳健且因其保守性可能驱动适当微生物群组装和功能的微生物群。为此，我们将来自八项研究的公开可用的肠道微生物群16S基因序列数据整合到一个系统发育树中，并确定了在个体中意外普遍存在的肠道细菌单系分支。这样做揭示了斑马鱼肠道中585个核心细菌分支，包括 、 、 、 、 、 、 和 内的分支。然后，我们应用线性回归来辨别这些核心分支中哪些对一系列不同的环境暴露敏感。我们发现200个核心分支对我们评估的任何暴露都不敏感，而134个核心分支对两种以上的暴露敏感。总体而言，我们的分析定义了斑马鱼核心肠道微生物群及其对暴露的敏感性，这有助于未来的研究评估其结果的稳健性，并为实证评估肠道微生物群如何介导暴露对斑马鱼宿主的影响确定优先研究的类群。
