Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut

Abstract

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, ...

Phages - bacteria interactions network of the healthy human gut

“…5 and Supplementary Table 3). All these contigs were unambiguously attributed to MAGs belonging to the Bacteroides clade, as expected from previous studies 13,48,49 . We notably detect Bacteroides vulgatus , Bacteroides uniformis, Bacteroides ovatus and Bacteroides thetaiotamicron as hosts of these crAss-like phages, four species already suspected to be the host of crAss-like phages.…”

“…CrAss-like phages are wide spread in human gut and are predicted to infect bacteria from the Bacteroides phylum but, so far, only one fully identified host has been described “in vitro” from one crAss member, Bacteroides intestinalis 13. We searched for the presence of crAss-like phages in our different assemblies using a set of previously reported representatives phages of this family 49 and detected 17 contigs, between 58 and 176 Kb, encoding proteins homologous to the crAss-like family proteins (Methods). Construction of a phylogenetic tree 45 encompassing these 17 contigs as well as different representatives of the crAss-like family 49 allowed us to find phages belonging to genera I, III, IV, VI and V (Fig.…”

ΦCrAss001, a member of the most abundant bacteriophage family in the human gut, infects Bacteroides

“…Tails are 36.1±3.6 nm long with elaborate structural features and several side appendages of variable length. This is in agreement with our previous TEM observations of podoviruses of similar dimensions (~76.5 nm in diameter) from a faecal sample rich in a mixture of several highly prevalent crAss-like bacteriophages 11 .…”

“…Based on electron microscopy of propagated crAssphage001 morphology we confirm that crAss-like phages possess podovirus-like morphology. We also demonstrate the ability of the phage to stably co-replicate with its Bacteroides intestinalis host in equilibrium for many generations in vitro, which mimics earlier observed ability of crAss-like phages to maintain stable colonization of the mammalian gut 11,12 .…”

“…Several recent studies identified a highly abundant (representing up to 90% of gut viruses in some individuals), unique uncultured group termed crAss-like phages or crAssphage [8][9][10][11] . Here we report on the first successful isolation of a crAssphage on a single host and describe its key biological properties.…”