Viral biogeography of the mammalian gut and parenchymal organs

Andrey N Shkoporov*, Stephen R Stockdale, Aonghus Lavelle, Ivanela Kondova, Cara Heuston, Aditya Upadrasta, Ekaterina V Khokhlova, Imme van der Kamp, Boudewijn Ouwerling, Lorraine A Draper, Jan A M Langermans, R Paul Ross, Colin Hill*

*Corresponding author for this work

    Research output: Contribution to journalArticleAcademicpeer-review


    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 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.

    Original languageEnglish
    Pages (from-to)1301-1311
    Number of pages11
    JournalNature Microbiology
    Issue number8
    Publication statusPublished - Aug 2022


    • Animals
    • Bacteriophages/genetics
    • Feces
    • Macaca mulatta
    • Mammals
    • Metagenome
    • Metagenomics
    • Viruses/genetics


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