Defining the human gut host-phage network through single-cell viral tagging

Nature Microbiology
Mária DžunkováPhilip Hugenholtz

Abstract

Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host-phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not maj...Continue Reading

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Citations

Sep 10, 2020·Cellular & Molecular Immunology·Sara FedericiEran Elinav
Mar 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Germán Bonilla-RossoPhilipp Engel
Aug 23, 2020·Viruses·Heyde MakimaaMegan T Baldridge
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Jul 6, 2020·Trends in Microbiology·Mohammadali Khan MirzaeiLi Deng
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Methods Mentioned

BETA
fluorescence-activated cell sorting
FACS
PCR
Assay
flow cytometry

Software Mentioned

CoverM
MEGAHIT
CRT
GNU
MAG
vegan
Accuri
SPAdes
SAMtools
DIAMOND

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