Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

Nature Microbiology
Natalya YutinEugene V Koonin

Abstract

Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery 1-3 . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome 4 . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study. Here we combine a comprehensive search of genomic and metagenomic databases with sensitive methods for protein sequence analysis to identify an expansive, diverse group of bacteriophages related to crAssphage and predict the functions of the majority of phage proteins, in particular those that comprise the structural, replication and expression modules. Most, if not all, of the crAss-like phages appear to be associated with diverse bacteria from the phylum Bacteroidetes, which includes some of the most abundant bacteria in the human...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Apr 23, 2003·Cell·Forest Rohwer
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Nov 9, 2004·Bioinformatics·Johannes Söding
Jun 28, 2005·Nucleic Acids Research·John Besemer, Mark Borodovsky
Jul 18, 2006·Nucleic Acids Research·Timothy L BaileyWilfred W Li
May 8, 2007·Nucleic Acids Research·William A ThompsonCharles E Lawrence
Sep 15, 2007·Nature Reviews. Microbiology·Curtis A Suttle
May 9, 2008·Molecular Biology and Evolution·Natalya YutinEugene V Koonin
Jul 9, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ye XiangMichael G Rossmann
Nov 10, 2009·Journal of Molecular Biology·William J Lane, Seth A Darst
Apr 3, 2010·Nucleic Acids Research·Gwenaël Ruprich-Robert, Pierre Thuriaux
Nov 6, 2010·Journal of Molecular Biology·Zhanna BerdygulovaLeonid Minakhin
Jun 28, 2011·The Journal of Biological Chemistry·Anshul BhardwajGino Cingolani
Nov 22, 2011·Nucleic Acids Research·David R KelleySteven L Salzberg
Jan 3, 2012·Journal of Structural Biology·Lakshminarayan M Iyer, L Aravind
Feb 3, 2012·Advances in Experimental Medicine and Biology·Sherwood R Casjens, Ian J Molineux
Jul 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Karin HolmfeldtMatthew B Sullivan
Jan 15, 2014·BMC Infectious Diseases·Bas B Oude MunninkLia van der Hoek
Jul 25, 2014·Nature Communications·Bas E DutilhRobert A Edwards
Jun 18, 2015·Nature·Christopher T BrownJillian F Banfield
Oct 7, 2015·Frontiers in Microbiology·Lesley A Ogilvie, Brian V Jones
Jan 1, 2014·Bacteriophage·Bas E Dutilh
Oct 21, 2015·Proceedings of the National Academy of Sciences of the United States of America·Jeremy J BarrForest Rohwer
Apr 1, 2016·FEMS Microbiology Letters·Bonnie L HurwitzKen Youens-Clark
Aug 31, 2016·Proceedings of the National Academy of Sciences of the United States of America·Pilar ManriqueMark J Young
Jan 31, 2017·Nature Reviews. Microbiology·Peter SimmondsF Murilo Zerbini
Mar 8, 2017·Proceedings of the National Academy of Sciences of the United States of America·Mart Krupovic, Eugene V Koonin
Apr 22, 2017·Cell·Weston R WhitakerJustin L Sonnenburg
Apr 26, 2017·Nature Microbiology·Aaron G Wexler, Andrew L Goodman

Citations

Mar 30, 2018·Viruses·Irene HuberWolfgang Beyer
Jun 19, 2018·Gut Microbes·Luisa De SordiLaurent Debarbieux
Oct 12, 2018·Nature Biotechnology·Charles Schmidt
Nov 20, 2018·Environmental Microbiology·Ying LiuDavid Prangishvili
Aug 29, 2019·Physiological Reviews·John F CryanTimothy G Dinan
Oct 17, 2019·Clinical Pharmacology and Therapeutics·Anukriti SharmaJack A Gilbert
Apr 16, 2020·International Journal of Molecular Sciences·Mario MatijašićDonatella Verbanac
Apr 21, 2020·Bioinformatics·Elizaveta V StarikovaVadim M Govorun
May 16, 2020·Bioinformatics·Dmitry AntipovPavel Pevzner
Jul 10, 2019·Nature Microbiology·Robert A EdwardsBas E Dutilh
Jun 20, 2018·Viruses·Marta LourençoLaurent Debarbieux
Jan 11, 2019·Microbiology and Molecular Biology Reviews : MMBR·Aislinn D Rowan-NashPeter Belenky
Jan 30, 2019·Nature Microbiology·Audra E DevotoJillian F Banfield
Nov 8, 2019·Alimentary Pharmacology & Therapeutics·João SabinoJean-Frederic Colombel
Oct 30, 2019·BMC Biology·Sanzhima GarmaevaAlexandra Zhernakova
Sep 23, 2020·Viruses·Alessandro RossiBas E Dutilh
Sep 27, 2020·Viruses·Maria L SokolovaKonstantin V Severinov
Apr 3, 2019·Therapeutic Advances in Gastroenterology·Indrani MukhopadhyaGeorgina L Hold
Jan 17, 2020·Nature Communications·Benjamin A SiranosianAmi S Bhatt
Sep 11, 2020·Nature Communications·Alaina R Weinheimer, Frank O Aylward
May 27, 2020·Evidence-based Complementary and Alternative Medicine : ECAM·Haojie YangZhenyi Wang
Jul 4, 2018·Journal of Immunology Research·Francesco Antonio SalzanoVincenzo Casolaro
Sep 13, 2018·Viruses·Claudio Hidalgo-CantabranaRodolphe Barrangou
Sep 6, 2018·The Journal of Immunology : Official Journal of the American Association of Immunologists·Jessica A Neil, Ken Cadwell
Dec 19, 2018·BMC Research Notes·Melany Cervantes-EcheverríaAdrián Ochoa-Leyva
Dec 19, 2019·Frontiers in Endocrinology·Thomas D S Sutton, Colin Hill
Mar 6, 2020·Microbiology and Molecular Biology Reviews : MMBR·Eugene V KooninJens H Kuhn
May 29, 2020·Nature·Guanxiang LiangFrederic D Bushman
Jul 22, 2020·Nature Microbiology·Yuri I WolfEugene V Koonin
Jun 6, 2018·Frontiers in Microbiology·Iris Fernández-RuizFrancisco Rodriguez-Valera
Oct 6, 2020·Frontiers in Cellular and Infection Microbiology·Emma Guerin, Colin Hill
Sep 26, 2020·Nucleic Acids Research·Darius KazlauskasČeslovas Venclovas
Oct 15, 2020·Scientific Data·Kira MoonJang-Cheon Cho
Jan 14, 2021·Scientific Reports·Yanpeng LiEric Delwart
Nov 12, 2020·Current Opinion in Biotechnology·Sofia DahlmanJeremy J Barr
Dec 12, 2020·Microorganisms·Antoni LuqueSimon White
Nov 20, 2020·Nature·Arina V DrobyshevaMaria L Sokolova
Feb 20, 2021·Gut Microbes·S CoughlanI B Jeffery
Feb 14, 2020·Cell Host & Microbe·Mohammadali Khan MirzaeiCorinne F Maurice
Mar 3, 2021·Current Opinion in Virology·Eugene V KooninMart Krupovic
Jul 31, 2018·Current Opinion in Microbiology·Anupriya TripathiRob Knight
Mar 18, 2021·Virus Evolution·Emma S EstermanOlga Zhaxybayeva
Mar 25, 2021·The Journal of Experimental Medicine·Yuhao LiMegan T Baldridge
Mar 31, 2021·Nature Reviews. Microbiology·Guanxiang Liang, Frederic D Bushman

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