Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14.

PloS One
Lesley A OgilvieBrian V Jones

Abstract

Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14). In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic anal...Continue Reading

References

Nov 5, 1975·Journal of Molecular Biology·G J PrussR Calendar
Feb 1, 1992·Computer Applications in the Biosciences : CABIOS·C Karreman
Dec 1, 1991·Nucleic Acids Research·N A LinderothR Calendar
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jul 1, 1987·Applied and Environmental Microbiology·C Tartera, J Jofre
Jan 1, 1968·Acta Pathologica Et Microbiologica Scandinavica·T Bergan, B Hovig
Jan 1, 1980·Annual Review of Microbiology·R A Warren
Jan 1, 1995·Annual Review of Biochemistry·C W Carreras, D V Santi
Nov 11, 1999·Nucleic Acids Research·A L DelcherS L Salzberg
Dec 20, 2000·Bioinformatics·K RutherfordB Barrell
Feb 15, 2001·JAMA : the Journal of the American Medical Association·H IsoW C Willett
Jul 4, 2001·Environmental Science & Technology·I Christl, R Kretzschmar
Jul 21, 2001·Journal of Acquired Immune Deficiency Syndromes : JAIDS·G M LucasR D Moore
Jun 5, 2002·Trends in Genetics : TIG·Eduardo P C Rocha, Antoine Danchin
Jun 11, 2002·International Journal of Systematic and Evolutionary Microbiology·Erko StackebrandtWilliam B Whitman
Nov 27, 2002·Applied and Environmental Microbiology·Troy M ScottJerzy Lukasik
Apr 23, 2003·Cell·Forest Rohwer
Jul 31, 2003·Molecular Microbiology·Sherwood Casjens
Oct 4, 2003·Journal of Bacteriology·Mya BreitbartForest Rohwer
Dec 23, 2003·Journal of Molecular Biology·Amy C Groth, Michele P Calos
Aug 13, 2004·Environmental Microbiology·Hanno TeelingFrank Oliver Glöckner
Nov 3, 2004·Genome Research·Zackary I Johnson, Sallie W Chisholm
Jun 25, 2005·Bioinformatics·Tim J CarverJulian Parkhill
Mar 24, 2006·FEMS Immunology and Medical Microbiology·Andrzej GórskiRyszard Miedzybrodzki
Mar 28, 2006·Experimental Biology and Medicine·Jan BorysowskiAndrzej Górski
Jun 3, 2006·Science·Steven R GillKaren E Nelson
Jun 23, 2006·Proceedings. Biological Sciences·Jaewook JooEric Harvill
Sep 8, 2006·Applied and Environmental Microbiology·Anicet R BlanchJoan Jofre
Nov 28, 2006·Nature Methods·Brian V Jones, Julian R Marchesi
Dec 15, 2006·BMC Ecology·Michael A BrockhurstPaul B Rainey
Apr 21, 2007·Nature Protocols·Olof EmanuelssonHenrik Nielsen
Jun 15, 2007·International Journal of Antimicrobial Agents·Geoffrey William Hanlon
Jun 21, 2007·PLoS Biology·Jian XuJeffrey I Gordon

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Citations

Jul 25, 2014·Nature Communications·Bas E DutilhRobert A Edwards
Jun 17, 2014·Environmental Science & Technology·Brian D ZimmermanDavid Wendell
Sep 17, 2013·Nature Communications·Lesley A OgilvieBrian V Jones
Oct 7, 2015·Frontiers in Microbiology·Lesley A Ogilvie, Brian V Jones
Mar 4, 2014·Water Research·Joan JofreMaite Muniesa
Jun 9, 2016·Journal of Clinical Medicine·Navena NavaneetharajaSimon R Carding
Aug 31, 2016·Proceedings of the National Academy of Sciences of the United States of America·Pilar ManriqueMark J Young
Dec 10, 2016·Gut Microbes·Felix BroeckerKarin Moelling
Sep 20, 2017·Microbial Biotechnology·Cristina García-AljaroJuan Jofre
Sep 5, 2017·Alimentary Pharmacology & Therapeutics·S R CardingL Hoyles
Jul 31, 2012·Journal of Virology·Ilnam KangJang-Cheon Cho
Jun 11, 2016·Annals of the New York Academy of Sciences·Felix BroeckerKarin Moelling
Aug 27, 2019·Frontiers in Microbiology·Diana R AlvesBrian V Jones
May 17, 2019·International Journal of Molecular Sciences·Shulin FuChien-An Andy Hu
Nov 30, 2017·Emerging Topics in Life Sciences·Lesley A Ogilvie, Brian V Jones
Jul 3, 2021·Viruses·Daniel Toribio-AvedilloLorena Rodríguez-Rubio
Jul 12, 2020·Cell Host & Microbe·Andrew J HryckowianJustin L Sonnenburg

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Datasets Mentioned

BETA
HE608159
HE608160
HE608841
SRA012183

Methods Mentioned

BETA
electrophoresis
PCR
restriction digest

Software Mentioned

Vector NTI Advance
Glimmer
Bioworks
Artemis Comparison Tool ( ACT )
Coregenes
BlastP
Gene Tools
Blastn
Prophinder
Artemis

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