(Simon Carding also leads the UK research on gut microbiota in ME at Quadram Science and Nadine Davis is one of the medical students funded by Invest in ME Research) Review article: the human intestinal virome in health and disease http://onlinelibrary.wiley.com/doi/10.1111/apt.14280/full Authors: S. R. Carding, N. Davis, L. Hoyles. First published: 4 September 2017 DOI: 10.1111/apt.14280 Funding information This study was funded in part by an institutional grant from the Biotechnology and Biological Sciences Research Council, grant number BB/J004529/1 (SRC), by an MRC Intermediate Research Fellowship in Data Science awarded to LH, and by a medical student research bursary from Invest In ME charity awarded to ND. This work used the computing resources of the UK MEDical BIOinformatics partnership—aggregation, integration, visualisation and analysis of large, complex data (UK MED-BIO), which is supported by the Medical Research Council, grant number MR/L01632X/1 The Handling Editor for this article was Professor Jonathan Rhodes, and this commissioned review was accepted for publication after full peer-review. Summary Background The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome. Aim To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases. Methods Relevant virome-related articles were selected for review following extensive language- and date-unrestricted, electronic searches of the literature. Results The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively. Conclusions Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome-disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions. ACKNOWLEDGEMENTS The authors would like to thank Sam Carding for creating Figure 1. Declaration of personal interest: None. AUTHORSHIP Guarantor of the article: Simon R. Carding. Author contributions: SRC takes responsibility for the integrity of the work as a whole, from inception to published article. LH and SRC designed the research study. LH and ND collected and analysed data. SRC and LH wrote the paper. All authors approve the final version of the manuscript.