Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

Environmental Microbiology
Margret E Berg MillerBryan A White

Abstract

Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of diversity was observed with up to 28,000 different viral genotypes obtained from each environment. The majority (~78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clus...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 1, 1988·Applied and Environmental Microbiology·D A StahlL Montgomery
Jun 1, 1988·Applied and Environmental Microbiology·A V Klieve, T Bauchop
Aug 1, 1982·Journal of Virology·B KwiatkowskiS Stirm
Jul 1, 1993·Applied and Environmental Microbiology·A V Klieve, R A Swain
Mar 1, 1996·Applied and Environmental Microbiology·R A SwainA V Klieve
Mar 21, 2000·Molecular Biology and Evolution·S Garcia-VallvéJ Palau
May 16, 2001·Science·J B Russell, J L Rychlik
Dec 26, 2001·Bioinformatics·H H Chou, M H Holmes
Oct 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Mya BreitbartForest Rohwer
Apr 23, 2003·Cell·Forest Rohwer
Aug 15, 2003·Nature·Nicholas H MannMartha Clokie
Sep 23, 2003·Proceedings of the National Academy of Sciences of the United States of America·Claudia BaarStephan C Schuster
Oct 4, 2003·Journal of Bacteriology·Mya BreitbartForest Rohwer
Nov 26, 2003·FEMS Microbiology Reviews·Denis O KrauseChristopher S McSweeney
Jul 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·Debbie LindellSallie W Chisholm
Sep 21, 2004·Nature Biotechnology·Soon Ho HongJae Jong Kim
Dec 21, 2004·Nature Structural & Molecular Biology·Katharina StummeyerRalf Ficner
Mar 29, 2005·Journal of Molecular Evolution·Francisco J M MojicaElena Soria
May 12, 2005·Nature Reviews. Microbiology·Robert E Edwards, Forest Rohwer
Jun 7, 2005·Trends in Microbiology·Mya Breitbart, Forest Rohwer
Jun 25, 2005·Bioinformatics·Tim J CarverJulian Parkhill
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Sep 3, 2005·Nature Reviews. Microbiology·Laura S FrostAriane Toussaint
Oct 11, 2005·Nucleic Acids Research·Ross A OverbeekVeronika Vonstein
Nov 9, 2006·PLoS Biology·Florent E AnglyForest Rohwer
Jun 1, 2007·Nucleic Acids Research·Ibtissem GrissaChristine Pourcel
Sep 11, 2007·Applied and Environmental Microbiology·Noah FiererRobert B Jackson
Dec 25, 2007·Nature Reviews. Microbiology·Rotem SorekPhilip Hugenholtz
Jan 9, 2008·Nature Reviews. Microbiology·Harry J FlintBryan A White
Feb 12, 2008·BMC Genomics·Ramy K AzizOlga Zagnitko
Mar 14, 2008·Nature·Elizabeth DinsdaleForest Rohwer
Oct 8, 2008·Nucleic Acids Research·Brandi L CantarelBernard Henrissat
Oct 25, 2008·Nucleic Acids Research·Eugene V Koonin, Yuri I Wolf
Feb 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jennifer M BrulcBryan A White
Mar 10, 2009·Applied and Environmental Microbiology·Niamh ToomeyDeclan Bolton
May 16, 2009·Nature·Forest Rohwer, Rebecca Vega Thurber
Oct 8, 2009·Molecular Biology and Evolution·Ofir Cohen, Tal Pupko
Oct 17, 2009·Nature Reviews. Microbiology·Francisco Rodriguez-ValeraAlex Mira
Nov 3, 2009·Environmental Microbiology·Forest RohwerDebbie Lindell
Feb 4, 2010·Nature Reviews. Genetics·Luciano A Marraffini, Erik J Sontheimer
Feb 12, 2010·The ISME Journal·Beltran Rodriguez-BritoForest Rohwer
Feb 16, 2010·Applied and Environmental Microbiology·Larissa C ParsleyMark R Liles
Mar 4, 2010·Microbiology and Molecular Biology Reviews : MMBR·Christian WinterT Frede Thingstad
Apr 3, 2010·Advances in Applied Microbiology·Paul Hyman, Stephen T Abedon
Jun 10, 2010·Annual Review of Microbiology·Hélène DeveauSylvain Moineau
Jul 16, 2010·Nature·Alejandro ReyesJeffrey I Gordon
Oct 12, 2010·PloS One·Nicole L HeldRachel J Whitaker
Jan 29, 2011·Science·Matthias HessEdward M Rubin
Aug 17, 2011·Frontiers in Microbiology·Rustam I Aminov

Citations

Jul 12, 2012·Applied Microbiology and Biotechnology·Sunil Kumar SirohiAnil Kumar Puniya
Nov 20, 2013·Applied Microbiology and Biotechnology·Sanjay KumarAnil Kumar Puniya
May 25, 2013·Animal Health Research Reviews·Bruce S SealCyril G Gay
Jun 14, 2013·Animal : an International Journal of Animal Bioscience·Sinead C LeahyGraeme T Attwood
Aug 7, 2012·Nature Reviews. Microbiology·Alejandro ReyesJeffrey I Gordon
Mar 21, 2012·Proceedings of the National Academy of Sciences of the United States of America·Aya Brown KavItzhak Mizrahi
Jul 10, 2012·Briefings in Bioinformatics·Tulika Prakash, Todd D Taylor
Nov 5, 2013·BMC Microbiology·Elizabeth M RossBen J Hayes
Mar 19, 2014·BMC Genomics·Anna A GoglevaIrena I Artamonova
Apr 15, 2014·Nucleic Acids Research·Krzysztof ChylinskiEugene V Koonin
Dec 15, 2015·FEMS Microbiology Reviews·Robert A EdwardsBas E Dutilh
Jun 9, 2015·Canadian Journal of Microbiology·N Shterzer, I Mizrahi
Apr 8, 2015·The ISME Journal·Jessica M LabontéRamunas Stepanauskas
Apr 16, 2014·Frontiers in Cellular and Infection Microbiology·Marianne De PaepeMarie-Agnès Petit
Apr 2, 2014·Frontiers in Microbiology·Leonard S van OverbeekPeter T J Willemsen
Nov 11, 2014·Annual Review of Animal Biosciences·Carl J Yeoman, Bryan A White
Aug 25, 2016·Environmental Microbiology·Sarah MoraïsEdward A Bayer
Nov 20, 2016·Molecular Ecology·Daniel MorleyStineke van Houte
Mar 9, 2017·BMC Microbiology·Alicia G BeukersTim A McAllister
Nov 29, 2017·Microbiome·Christopher L AndersonSamodha C Fernando
Jun 19, 2014·Bioinformatics and Biology Insights·Joshua C McCannJuan J Loor
Jan 1, 2012·Biochemistry Insights·Hongjun JinPhilip E Long
Jun 19, 2018·Journal of Clinical Gastroenterology·Gianenrico RizzattiA Gasbarrini
Jul 18, 2019·FEMS Microbiology Letters·Thomas C A HitchRosalind A Gilbert
Aug 27, 2018·Journal of Cellular Biochemistry·Zhirui ZhangWu Yin
Feb 14, 2014·Cancer Biology & Therapy·Cristina RaimondiPaola Gazzaniga
Oct 26, 2018·Nature Microbiology·Lindsey M SoldenKelly C Wrighton
Oct 24, 2015·BMC Genomics·R John WallaceRainer Roehe
Apr 26, 2017·Frontiers in Microbiology·Krupa M ParmarRavindra Pal Singh
Apr 11, 2020·Frontiers in Microbiology·Rosalind A GilbertEleanor Jameson
Dec 24, 2019·Frontiers in Microbiology·Mohammad Mazharul IslamRajib Saha
Aug 8, 2020·Frontiers in Microbiology·Jessica C A FriedersdorffChristopher J Creevey
Dec 13, 2017·BioMed Research International·G RizzattiA Gasbarrini
Jul 24, 2019·Journal of Animal Science and Technology·Mahfuzul Islam, Sang-Suk Lee

Related Concepts

Bacteriophages
Bos indicus
DNA, Bacterial
DNA, Viral
Rumen
Sequence Determinations, DNA
Computational Molecular Biology
Interspersed Repetitive Sequences
Biodiversity
Microbiome

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