ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis.
Andrey N. Shkoporov,Ekaterina V. Khokhlova,C. Brian Fitzgerald,Stephen R. Stockdale,Lorraine A. Draper,R. Paul Ross,R. Paul Ross,Colin Hill +7 more
TLDR
Bacteriophages of the crAssphage family have not yet been isolated in culture and it is shown that it infects the human gut symbiont Bacteroides intestinalis, confirming previous in silico predictions of the likely host.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. Bacteriophages of the crAssphage family have not yet been isolated, despite being highly abundant in the human gut. Here, Shkoporov et al. isolate in pure culture one of these viruses and show that it infects the human gut symbiont Bacteroides intestinalis.read more
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Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
Andrey N. Shkoporov,Colin Hill +1 more
TL;DR: This Review summarizes the available methods and main findings regarding taxonomic composition, community structure, and population dynamics in the human gut phageome, and discusses the main challenges in the field and identify promising avenues for future research.
Journal ArticleDOI
The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific
Andrey N. Shkoporov,Adam G. Clooney,Thomas D.S. Sutton,Feargal J. Ryan,Karen Daly,James A. Nolan,Siobhan A. McDonnell,Ekaterina V. Khokhlova,Lorraine A. Draper,Amanda Forde,Emma Guerin,Vimalkumar Velayudhan,R. Paul Ross,Colin Hill +13 more
TL;DR: This study performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome.
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Global Organization and Proposed Megataxonomy of the Virus World
Eugene V. Koonin,Valerian V. Dolja,Mart Krupovic,Arvind Varsani,Arvind Varsani,Yuri I. Wolf,Natalya Yutin,F. Murilo Zerbini,Jens H. Kuhn +8 more
TL;DR: Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase, and propose a comprehensive hierarchical taxonomy of viruses.
Journal ArticleDOI
Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments
TL;DR: It is found that the presence of resistance genes can largely be explained by fecal pollution, with no clear signs of selection in the environment, with the exception of environments polluted by very high levels of antibiotics from manufacturing, where selection is evident.
Journal ArticleDOI
Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease
Adam G. Clooney,Thomas D.S. Sutton,Andrey N. Shkoporov,Ross K. Holohan,Karen Daly,Orla O’Regan,Feargal J. Ryan,Lorraine A. Draper,Scott E. Plevy,R. Paul Ross,Colin Hill +10 more
TL;DR: In this article, the authors performed whole-virome analysis on a published keystone inflammatory bowel disease (IBD) cohort and an in-house ulcerative colitis dataset to shed light on the composition of the human gut virome in IBD beyond this identifiable minority.
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