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.
Highlights
CrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales
Based on electron microscopy of propagated crAss[001], we confirm that crAss-like bacteriophages possess podovirus-like morphology
We attempted to detect crAss-like bacteriophage replication using a broth enrichment strategy
Summary
CrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales. 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. In the absence of a known host, no member of this family has been isolated and nothing is known of the biological properties of these crAss-like viruses from the human gut. In a recent analysis[13], we de novo-assembled 244 genomes of crAss-like bacteriophages from the human gut and classified them into 10 genus- and 4 subfamily-level taxonomic groups (Alphacrassvirinae, Betacrassvirinae, Gammacrassvirinae and Deltacrassvirinae) based on percentage of shared orthologous genes. We demonstrate the ability of the virus to stably co-replicate with its Bacteroides intestinalis host in equilibrium for many generations in vitro, which mimics earlier observed ability of crAss-like bacteriophages to maintain stable colonisation of the mammalian gut[13,14]
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