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Article

Phylogenetic Integration Reveals the Zebrafish Core Microbiome and Its Sensitivity to Environmental Exposures

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Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
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Department of Statistics, Oregon State University, Corvallis, OR 97331, USA
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Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
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Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA
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Author to whom correspondence should be addressed.
Toxics 2021, 9(1), 10; https://doi.org/10.3390/toxics9010010
Received: 5 December 2020 / Revised: 8 January 2021 / Accepted: 11 January 2021 / Published: 15 January 2021
(This article belongs to the Special Issue Advanced Zebrafish Model for Environmental Health Sciences Research)
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 Aeromonas, Pseudomonas, Cetobacterium, Shewanella, Chitinibacter, Fluviicola, Flectobacillus, and Paucibacter. 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. View Full-Text
Keywords: zebrafish; gut microbiome; environmental exposure; phylogenetics; meta-analysis zebrafish; gut microbiome; environmental exposure; phylogenetics; meta-analysis
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MDPI and ACS Style

Sharpton, T.J.; Stagaman, K.; Sieler, M.J., Jr.; Arnold, H.K.; Davis, E.W., II. Phylogenetic Integration Reveals the Zebrafish Core Microbiome and Its Sensitivity to Environmental Exposures. Toxics 2021, 9, 10. https://doi.org/10.3390/toxics9010010

AMA Style

Sharpton TJ, Stagaman K, Sieler MJ Jr., Arnold HK, Davis EW II. Phylogenetic Integration Reveals the Zebrafish Core Microbiome and Its Sensitivity to Environmental Exposures. Toxics. 2021; 9(1):10. https://doi.org/10.3390/toxics9010010

Chicago/Turabian Style

Sharpton, Thomas J., Keaton Stagaman, Michael J. Sieler Jr., Holly K. Arnold, and Edward W. Davis II. 2021. "Phylogenetic Integration Reveals the Zebrafish Core Microbiome and Its Sensitivity to Environmental Exposures" Toxics 9, no. 1: 10. https://doi.org/10.3390/toxics9010010

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