ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

Abstract

CrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales. Despite being found in ~50% of individuals and representing up to 90% of human gut viromes, members of this viral family have never been isolated in culture and remain understudied. Here, we report the isolation of a CrAssphage (ΦCrAss001) from human faecal material. This bacteriophage infects the human gut symbiont Bacteroides intestinalis, confirming previous in silico predictions of the likely host. DNA sequencing demonstrates that the bacteriophage genome is circular, 102 kb in size, and has unusual structural traits. In addition, electron microscopy confirms that ΦcrAss001 has a podovirus-like morphology. Despite the absence of obvious lysogeny genes, ΦcrAss001 replicates in a way that does not disrupt proliferation of the host bacterium, and is able to maintain itself in continuous host culture during several weeks.

Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

“…Although a crAss-like phage similar to cluster Beta 06 phages was recently cultured on a Bacteroides intestinalis host 20 , the hosts of other crAss-like phages have yet to be identified. We searched for bacterial taxa that were differentially abundant between crAss-like phage positive and negative infants to make inferences about potential hosts.…”

5 challenges in understanding the role of the virome in health and disease

“…As an example, although dozens of novel eukaryotic viruses have been identified in the mammalian enteric tract by metagenomic sequencing, culture systems for only a very limited number have been described to date [14,15]. Likewise, for phages, genomic sequences of thousands of novel phages can be identified in a single study [16,17], but very few have been isolated [18]. Thus, while (in the past) discovery of novel viruses was rate limiting, today the rate-limiting step has shifted to development of culture systems for the viruses that have been molecularly identified.…”

Review article: bacteriophages in gastroenterology—from biology to clinical applications

“…The healthy human gut virome is characterised by low intrapersonal diversity and dominated by temperate phages . The recently described family of phages, CrAssphages, are the most abundant viruses in the human gut and are believed to infect bacteria of the order Bacteroidales …”

“…40 The recently described family of phages, CrAssphages, are the most abundant viruses in the human gut and are believed to infect bacteria of the order Bacteroidales. [41][42][43] The role of phages in IBD-associated dysbiosis has long been suggested. 44 Patients with Crohn's disease or ulcerative colitis have abnormal gut viromes with an increase in the Caudovirales to Microviridae ratio, which is paralleled by a decrease in bacterial richness and diversity.…”