Highlights d The human gut virome is highly individual and stable for up to 1 year d A stable and predominant fraction of viruses constitutes a persistent personal virome d Persistent bacteriophages can be linked to highly predominant gut bacterial taxa d Virulent crAss-like and Microviridae bacteriophages predominate and persist in the gut

The human gut virome is thought to significantly impact the microbiome and human health. However, most virome analyses have been performed on a limited fraction of known viruses. Using whole-virome analysis on a published keystone inflammatory bowel disease (IBD) cohort and an in-house ulcerative colitis dataset, we shed light on the composition of the human gut virome in IBD beyond this identifiable minority. We observe IBD-specific changes to the virome and increased numbers of temperate phage sequences in individuals with Crohn's disease. Unlike prior database-dependent methods, no changes in viral richness were observed. Among IBD subjects, the changes in virome composition reflected alterations in bacterial composition. Furthermore, incorporating both bacteriome and virome composition offered greater classification power between health and disease. This approach to analyzing whole virome across cohorts highlights significant IBD signals, which may be crucial for developing future biomarkers and therapeutics.

17CrAssphage is yet to be cultured even though it represents the most abundant virus in 18 the gut microbiota of humans. Recently, sequence based classification was performed on 19 distantly related crAss-like phages from multiple environments, leading to the proposal of a 20 familial level taxonomic group [Yutin N, et al. (2018) Discovery of an expansive 21 bacteriophage family that includes the most abundant viruses from the human gut. Nat 22 Microbiol 3(1):38-46]. Here, we assembled the metagenomic sequencing reads from 702 23 human faecal virome/phageome samples and obtained 98 complete circular crAss-like phage 24 genomes and 145 contigs ≥70kb. In silico comparative genomics and taxonomic analysis was 25 performed, resulting in a classification scheme of crAss-like phages from human faecal 26 microbiomes into 4 candidate subfamilies composed of 10 candidate genera. Moreover, 27 laboratory analysis was performed on faecal samples from an individual harbouring 7 distinct 28 crAss-like phages. We achieved propagation of crAss-like phages in ex vivo human faecal 29 fermentations and visualised Podoviridae virions by electron microscopy. Furthermore, 30 detection of a crAss-like phage capsid protein could be linked to metagenomic sequencing 31 data confirming crAss-like phage structural annotations. 32 33 34 35 36 37 38 39 40 41 3 Significance 42CrAssphage is the most abundant biological entity in the human gut, but it remains 43 uncultured in the laboratory and its host(s) is unknown. CrAssphage was not identified in 44 metagenomic studies for many years as its sequence is so different from anything present in 45 databases. To this day, it can only be detected from sequences assembled from metagenomics 46 or viromic datasets (crAsscross Assembly). In this study, we identified 243 new crAss-like 47 phages from human faecal metagenomic studies. Taxonomic analysis of these crAss-like 48 phages highlighted their extensive diversity within the human microbiome. We also present 49 the first propagation of crAssphage in faecal fermentations and provide the first electron 50 micrographs of this extraordinary bacteriophage. 51 52 53In recent years, increasing numbers of bacteria, archaea, fungi, protists and viruses 54 residing on and within the human body have been associated with various states of human 55 health and disease, including diet, age, weight, inflammatory bowel disease (IBD), diabetes, 56 and cognition (1-7). A relatively small number of eukaryote viruses present in the 57 gastrointestinal tract can target the human host, however, much larger and much more 58 complex populations of viruses that target bacteria (bacteriophages) also reside there. The 59 role of phages in the gut has been a subject of increased interest as initial investigations have 60 revealed substantial differences in bacteriophage populations between healthy and diseased 61 cohorts (7-11). It is likely that phages have an important role in shaping our gut microbiome, 62 but their precise role remains poorly understood. 63In 2014, ...