Viral biogeography of the mammalian gut and parenchymal organs
Shkoporov, Andrey N; Stockdale, Stephen R; Lavelle, Aonghus; Kondova, Ivanela; Heuston, Cara; Upadrasta, Aditya; Khokhlova, Ekaterina V; van der Kamp, Imme; Ouwerling, Boudewijn; Draper, Lorraine A; Langermans, Jan A M; Paul Ross, R; Hill, Colin
(2022) Nature Microbiology, volume 7, issue 8, pp. 1301 - 1311
(Article)
Abstract
The mammalian virome has been linked to health and disease but our understanding of how it is structured along the longitudinal axis of the mammalian gastrointestinal tract (GIT) and other organs is limited. Here, we report a metagenomic analysis of the prokaryotic and eukaryotic virome occupying luminal and mucosa-associated habitats
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along the GIT, as well as parenchymal organs (liver, lung and spleen), in two representative mammalian species, the domestic pig and rhesus macaque (six animals per species). Luminal samples from the large intestine of both mammals harboured the highest loads and diversity of bacteriophages (class Caudoviricetes, family Microviridae and others). Mucosal samples contained much lower viral loads but a higher proportion of eukaryotic viruses (families Astroviridae, Caliciviridae, Parvoviridae). Parenchymal organs contained bacteriophages of gut origin, in addition to some eukaryotic viruses. Overall, GIT virome composition was specific to anatomical region and host species. Upper GIT and mucosa-specific viruses were greatly under-represented in distal colon samples (a proxy for faeces). Nonetheless, certain viral and phage species were ubiquitous in all samples from the oral cavity to the distal colon. The dataset and its accompanying methodology may provide an important resource for future work investigating the biogeography of the mammalian gut virome.
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Keywords: Animals, Bacteriophages/genetics, Feces, Macaca mulatta, Mammals, Metagenome, Metagenomics, Viruses/genetics, Taverne
ISSN: 1740-1526
Publisher: Nature Publishing Group
Note: Funding Information: This research was conducted with the financial support of Science Foundation Ireland (SFI) under grant number SFI/12/RC/2273 (C. Hill and R.P.R.), an SFI's Spokes Programme which is co-funded under the European Regional Development Fund under grant number SFI/14/SP APC/B3032, Wellcome Trust Research Career Development Fellowship (220646/Z/20/Z0) (A.N.S.); and a research grant from Janssen Biotech, Inc. (C. Hill and R.P.R.). This research was funded in whole, or in part, by the Wellcome Trust (220646/Z/20/Z). For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. We thank T. Haaksma (BPRC) for his technical help with animal sampling, as well as J. Fitzgerald and J. Eckenberger for the fruitful discussion of statistical methods used in the study. The schematics in Figs. – were created with BioRender.com. Publisher Copyright: © 2022, The Author(s), under exclusive licence to Springer Nature Limited.
(Peer reviewed)