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

Emma Guerin, Andrey Shkoporov, Stephen R. Stockdale, Adam G. Clooney, Feargal J. Ryan, Lorraine A. Draper, Enrique Gonzalez-Tortuero, R. Paul Ross, Colin Hill
doi: https://doi.org/10.1101/295642
Emma Guerin
aAPC Microbiome Ireland, University College Cork, Co. Cork, Ireland
bSchool of Microbiology, University College Cork, Co. Cork, Ireland
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Andrey Shkoporov
aAPC Microbiome Ireland, University College Cork, Co. Cork, Ireland
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Stephen R. Stockdale
aAPC Microbiome Ireland, University College Cork, Co. Cork, Ireland
cTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
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Adam G. Clooney
aAPC Microbiome Ireland, University College Cork, Co. Cork, Ireland
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Feargal J. Ryan
aAPC Microbiome Ireland, University College Cork, Co. Cork, Ireland
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Lorraine A. Draper
aAPC Microbiome Ireland, University College Cork, Co. Cork, Ireland
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Enrique Gonzalez-Tortuero
aAPC Microbiome Ireland, University College Cork, Co. Cork, Ireland
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R. Paul Ross
aAPC Microbiome Ireland, University College Cork, Co. Cork, Ireland
bSchool of Microbiology, University College Cork, Co. Cork, Ireland
cTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
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Colin Hill
aAPC Microbiome Ireland, University College Cork, Co. Cork, Ireland
bSchool of Microbiology, University College Cork, Co. Cork, Ireland
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Abstract

CrAssphage is yet to be cultured even though it represents the most abundant virus in the gut microbiota of humans. Recently, sequence based classification was performed on distantly related crAss-like phages from multiple environments, leading to the proposal of a familial level taxonomic group [Yutin N, et al. (2018) Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat Microbiol 3(1):38–46]. Here, we assembled the metagenomic sequencing reads from 702 human faecal virome/phageome samples and obtained 98 complete circular crAss-like phage genomes and 145 contigs ≥70kb. In silico comparative genomics and taxonomic analysis was performed, resulting in a classification scheme of crAss-like phages from human faecal microbiomes into 4 candidate subfamilies composed of 10 candidate genera. Moreover, laboratory analysis was performed on faecal samples from an individual harbouring 7 distinct crAss-like phages. We achieved propagation of crAss-like phages in ex vivo human faecal fermentations and visualised Podoviridae virions by electron microscopy. Furthermore, detection of a crAss-like phage capsid protein could be linked to metagenomic sequencing data confirming crAss-like phage structural annotations.

Significance CrAssphage is the most abundant biological entity in the human gut, but it remains uncultured in the laboratory and its host(s) is unknown. CrAssphage was not identified in metagenomic studies for many years as its sequence is so different from anything present in databases. To this day, it can only be detected from sequences assembled from metagenomics or viromic datasets (crAss – cross Assembly). In this study, we identified 243 new crAss-like phages from human faecal metagenomic studies. Taxonomic analysis of these crAss-like phages highlighted their extensive diversity within the human microbiome. We also present the first propagation of crAssphage in faecal fermentations and provide the first electron micrographs of this extraordinary bacteriophage.

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Posted April 06, 2018.
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Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut
Emma Guerin, Andrey Shkoporov, Stephen R. Stockdale, Adam G. Clooney, Feargal J. Ryan, Lorraine A. Draper, Enrique Gonzalez-Tortuero, R. Paul Ross, Colin Hill
bioRxiv 295642; doi: https://doi.org/10.1101/295642
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Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut
Emma Guerin, Andrey Shkoporov, Stephen R. Stockdale, Adam G. Clooney, Feargal J. Ryan, Lorraine A. Draper, Enrique Gonzalez-Tortuero, R. Paul Ross, Colin Hill
bioRxiv 295642; doi: https://doi.org/10.1101/295642

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