title: Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines.
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.
authors.affiliation: KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium.
authors.forename: Mireia
authors.initials: M
authors.lastname: Valles-Colomer
authors.affiliation: KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
authors.forename: Youssef
authors.initials: Y
authors.lastname: Darzi
authors.affiliation: KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium.
authors.forename: Sara
authors.initials: S
authors.lastname: Vieira-Silva
authors.affiliation: KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium.
authors.forename: Gwen
authors.initials: G
authors.lastname: Falony
authors.affiliation: KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.affiliation: KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
authors.forename: Marie
authors.initials: M
authors.lastname: Joossens
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D004269:DNA, Bacterial / Q000032:analysis; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D016678:Genome; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology*; D056186:Metagenomics; D020543:Proteome; D040901:Proteomics; D012329:RNA, Bacterial / Q000032:analysis; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D020543:Proteome; D012329:RNA, Bacterial
keywords: 16S; Metagenomics; meta-omics; metaproteomics; metatranscriptomics; microbiota