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.

哺乳动物病毒组与健康和疾病有关，但我们对它如何沿哺乳动物胃肠道 (GIT) 和其他器官的纵轴构成的了解有限。在这里，我们报告了对占据 GIT 管腔和粘膜相关栖息地的原核和真核病毒组的宏基因组分析，以及两种具有代表性的哺乳动物物种家猪和恒河猴的实质器官（肝、肺和脾）。每个物种六只动物）。来自两种哺乳动物大肠的管腔样本都含有最高的噬菌体负载和多样性（有尾噬菌体类、微病毒科等）。粘膜样本含有低得多的病毒载量，但真核病毒（家族星状病毒科、杯状病毒科、细小病毒科）。除了一些真核病毒外，实质器官还含有肠道来源的噬菌体。总体而言，GIT 病毒组的组成特定于解剖区域和宿主物种。上消化道和粘膜特异性病毒在远端结肠样本（粪便的代表）中的代表性大大不足。尽管如此，某些病毒和噬菌体种类在从口腔到远端结肠的所有样本中无处不在。该数据集及其附带的方法可能为未来研究哺乳动物肠道病毒组生物地理学的工作提供重要资源。