Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines

Journal of Crohn's & Colitis
Mireia Valles-ColomerJeroen Raes

Abstract

Meta-omics [metagenomics, metatranscriptomics, and metaproteomics] are rapidly expanding our knowledge of the gut microbiota in health and disease. These technologies are increasingly used in inflammatory bowel disease [IBD] research. Yet, meta-omics data analysis, interpretation, and among-study comparison remain challenging. In this review we discuss the role these techniques are playing in IBD research, highlighting their strengths and limitations. We give guidelines on proper sample collection and preparation methods, and on performing the analyses and interpreting the results, reporting available user-friendly tools and pipelines.

References

Oct 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·D J LaneN R Pace
Dec 3, 1998·Gastroenterology·A Darfeuille-MichaudJ F Colombel
Dec 11, 1999·Nucleic Acids Research·R L TatusovE V Koonin
Jul 21, 2004·Bioinformatics·Marshall BernJohn R Yates
Apr 16, 2005·Science·Paul B EckburgDavid A Relman
Jul 5, 2006·EMBO Reports·Ann M O'Hara, Fergus Shanahan
Jul 6, 2006·Applied and Environmental Microbiology·T Z DeSantisG L Andersen
Apr 5, 2007·Nature Protocols·Erwin G ZoetendalWillem M de Vos
Aug 19, 2007·Proceedings of the National Academy of Sciences of the United States of America·Daniel N FrankNorman R Pace
Apr 11, 2008·The ISME Journal·Johan DicksvedJanet K Jansson
Oct 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Harry SokolPhilippe Langella
Oct 31, 2008·The ISME Journal·Nathan C VerberkmoesJanet K Jansson
Feb 6, 2009·Bioinformatics·Lukas KällWilliam Stafford Noble
Mar 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Michael A MahowaldJeffrey I Gordon
Aug 15, 2009·PLoS Computational Biology·Yuzhen Ye, Thomas G Doak
Jan 22, 2010·PLoS Genetics·Sara Vieira-Silva, Eduardo P C Rocha
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Jan 7, 2011·BMC Genomics·Koos RooijersPeter J Schaap
Feb 2, 2011·PloS One·Sebastian RealAlbert Tauler
Apr 22, 2011·Nature·Manimozhiyan ArumugamPeer Bork
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Nov 22, 2011·Nucleic Acids Research·David R KelleySteven L Salzberg
Dec 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sharon GreenblumElhanan Borenstein
Apr 24, 2012·Nature Biotechnology·Nicholas J LomanMark J Pallen
Jun 13, 2012·Nature Methods·Nicola SegataCurtis Huttenhower
Jun 16, 2012·Nature·UNKNOWN Human Microbiome Project Consortium
Jun 22, 2012·PLoS Computational Biology·Sahar AbubuckerCurtis Huttenhower
Jul 17, 2012·Nature Reviews. Microbiology·Karoline Faust, Jeroen Raes
Jul 19, 2012·PLoS Computational Biology·Karoline FaustCurtis Huttenhower
Aug 1, 2012·BMC Microbiology·Silvia CardonaChaysavanh Manichanh

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Citations

Apr 12, 2016·Frontiers in Microbiology·Sylvie SchulzeJörg Linde
Apr 30, 2016·Expert Review of Molecular Diagnostics·Thomas ClavelAndreas Hiergeist
Dec 9, 2016·Omics : a Journal of Integrative Biology·Orazio PalmieriAnna Latiano
Oct 12, 2018·Journal of Crohn's & Colitis·Javier P Gisbert, María Chaparro
Jul 20, 2019·Proteomics·Danielle L PetersDaniel Figeys
Feb 9, 2018·Frontiers in Microbiology·Kevin D'hoeJeroen Raes
Mar 14, 2017·Frontiers in Cellular and Infection Microbiology·Shaocun ZhangHe Huang
Dec 27, 2016·Frontiers in Physiology·Alejandra V ContrerasOsbaldo Resendis-Antonio
Sep 1, 2018·World Journal of Gastroenterology : WJG·Jason ReinglasPeter L Lakatos
Nov 24, 2018·Scientific Reports·Aina E Fossum MoenUNKNOWN IBD-Character Consortium
Jan 4, 2021·Journal of Crohn's & Colitis·Vipin GuptaJack Satsangi
Jul 4, 2021·Neuroscience Bulletin·Xueling ZhuLanjuan Li
Aug 5, 2021·Journal of Crohn's & Colitis·Roger FeakinsMonika Tripathi

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