Viral biogeography of the mammalian gut and parenchymal organs

Little is known on how the gastrointestinal virome is structured along the longitudinal axis of the mammalian digestive system. In this study we report a comprehensive metagenomic analysis of the prokaryotic and eukaryotic virome occupying luminal and mucosa-associated habitats along the length of the gastrointestinal tract (GIT) in two representative mammalian species, the domestic pig and rhesus macaque (six animals of each species), chosen for their relevance to humans. The highest loads and diversity of bacteriophages (class Caudoviricetes, family Microviridae and others) were detected in the lumen of the large intestine in both mammals. Mucosal samples contained much lower viral loads but a higher proportion of eukaryotic viruses (families Astroviridae, Caliciviridae, Parvoviridae). Parenchymal organs (liver, lung and spleen) contained significant numbers of bacteriophages of gut origin, in addition to some eukaryotic viruses. GIT virome composition is both region- and species-specific and is distinct between upper and lower gut. Upper GIT and mucosa-specific viruses are greatly under-represented in distal colon samples, which is used as a proxy for faeces. Nonetheless, certain viral and phage species are found ubiquitously 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.