title: Dynamics of the human gut microbiome in inflammatory bowel disease.
abstract: Inflammatory bowel disease (IBD) is characterized by flares of inflammation with a periodic need for increased medication and sometimes even surgery. The aetiology of IBD is partly attributed to a deregulated immune response to gut microbiome dysbiosis. Cross-sectional studies have revealed microbial signatures for different IBD subtypes, including ulcerative colitis, colonic Crohn's disease and ileal Crohn's disease. Although IBD is dynamic, microbiome studies have primarily focused on single time points or a few individuals. Here, we dissect the long-term dynamic behaviour of the gut microbiome in IBD and differentiate this from normal variation. Microbiomes of IBD subjects fluctuate more than those of healthy individuals, based on deviation from a newly defined healthy plane (HP). Ileal Crohn's disease subjects deviated most from the HP, especially subjects with surgical resection. Intriguingly, the microbiomes of some IBD subjects periodically visited the HP then deviated away from it. Inflammation was not directly correlated with distance to the healthy plane, but there was some correlation between observed dramatic fluctuations in the gut microbiome and intensified medication due to a flare of the disease. These results will help guide therapies that will redirect the gut microbiome towards a healthy state and maintain remission in IBD.
authors.affiliation: Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro SE-701 82, Sweden.
authors.forename: Jonas
authors.identifier: http://orcid.org/0000-0003-0122-7234
authors.initials: J
authors.lastname: Halfvarson
authors.affiliation: Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA.
authors.forename: Colin J
authors.initials: CJ
authors.lastname: Brislawn
authors.affiliation: Juniata College, Huntingdon, Pennsylvania 16652, USA.
authors.forename: Regina
authors.initials: R
authors.lastname: Lamendella
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Vázquez-Baeza
authors.affiliation: Max Planck Institute, 72076 Tübingen, Germany.
authors.forename: William A
authors.initials: WA
authors.lastname: Walters
authors.affiliation: National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA.
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Bramer
authors.affiliation: Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, SE-171 76 Stockholm, Sweden.|BioDonostia Health Research Institute San Sebastian, and IKERBASQUE Basque Foundation for Science Bilbao 48011, Spain.
authors.forename: Mauro
authors.initials: M
authors.lastname: D'Amato
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77, Stockholm Sweden.
authors.forename: Ferdinando
authors.initials: F
authors.lastname: Bonfiglio
authors.affiliation: Department of Pediatrics, University of California, San Diego, California 92093, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: McDonald
authors.affiliation: Center for Microbiome Innovation, University of California, San Diego, California 92093, USA.
authors.forename: Antonio
authors.initials: A
authors.lastname: Gonzalez
authors.affiliation: Juniata College, Huntingdon, Pennsylvania 16652, USA.
authors.forename: Erin E
authors.initials: EE
authors.lastname: McClure
authors.affiliation: Juniata College, Huntingdon, Pennsylvania 16652, USA.
authors.forename: Mitchell F
authors.initials: MF
authors.lastname: Dunklebarger
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.|Department of Pediatrics, University of California, San Diego, California 92093, USA.|Center for Microbiome Innovation, University of California, San Diego, California 92093, USA.
authors.forename: Rob
authors.identifier: http://orcid.org/0000-0002-0975-9019
authors.initials: R
authors.lastname: Knight
authors.affiliation: Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA.
authors.forename: Janet K
authors.initials: JK
authors.lastname: Jansson
mesh_terms: D000328:Adult; D003093:Colitis, Ulcerative / Q000382:microbiology; D003424:Crohn Disease / Q000382:microbiology; D003430:Cross-Sectional Studies; D064806:Dysbiosis / Q000276:immunology / Q000382:microbiology*; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome / Q000235:genetics / Q000502:physiology*; D006801:Humans; D007249:Inflammation / Q000382:microbiology; D015212:Inflammatory Bowel Diseases / Q000276:immunology / Q000382:microbiology* / Q000503:physiopathology; D039841:Leukocyte L1 Antigen Complex / Q000032:analysis; D008297:Male; D010641:Phenotype
chemical_list: D039841:Leukocyte L1 Antigen Complex