title: Disease-specific alterations in the enteric virome in inflammatory bowel disease.
abstract: Decreases in the diversity of enteric bacterial populations are observed in patients with Crohn's disease (CD) and ulcerative colitis (UC). Less is known about the virome in these diseases. We show that the enteric virome is abnormal in CD and UC patients. In-depth analysis of preparations enriched for free virions in the intestine revealed that CD and UC were associated with a significant expansion of Caudovirales bacteriophages. The viromes of CD and UC patients were disease and cohort specific. Importantly, it did not appear that expansion and diversification of the enteric virome was secondary to changes in bacterial populations. These data support a model in which changes in the virome may contribute to intestinal inflammation and bacterial dysbiosis. We conclude that the virome is a candidate for contributing to, or being a biomarker for, human inflammatory bowel disease and speculate that the enteric virome may play a role in other diseases.
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Norman
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Handley
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Megan T
authors.initials: MT
authors.lastname: Baldridge
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Lindsay
authors.initials: L
authors.lastname: Droit
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Catherine Y
authors.initials: CY
authors.lastname: Liu
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Keller
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Amal
authors.initials: A
authors.lastname: Kambal
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Cynthia L
authors.initials: CL
authors.lastname: Monaco
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
authors.forename: Guoyan
authors.initials: G
authors.lastname: Zhao
authors.affiliation: Division of Colorectal Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
authors.forename: Phillip
authors.initials: P
authors.lastname: Fleshner
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Thaddeus S
authors.initials: TS
authors.lastname: Stappenbeck
authors.affiliation: The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
authors.forename: Dermot P B
authors.initials: DP
authors.lastname: McGovern
authors.affiliation: Department of Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL 60612, USA.
authors.forename: Ali
authors.initials: A
authors.lastname: Keshavarzian
authors.affiliation: Department of Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL 60612, USA.
authors.forename: Ece A
authors.initials: EA
authors.lastname: Mutlu
authors.affiliation: Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Jenny
authors.initials: J
authors.lastname: Sauk
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.affiliation: Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Ramnik J
authors.initials: RJ
authors.lastname: Xavier
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
authors.forename: David
authors.initials: D
authors.lastname: Wang
authors.affiliation: Division of Gastroenterology Addenbrooke's Hospital and Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
authors.forename: Miles
authors.initials: M
authors.lastname: Parkes
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: virgin@wustl.edu.
authors.forename: Herbert W
authors.initials: HW
authors.lastname: Virgin
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D016022:Case-Control Studies; D017899:Caudovirales / Q000235:genetics / Q000302:isolation & purification*; D015331:Cohort Studies; D003093:Colitis, Ulcerative / Q000382:microbiology / Q000473:pathology / Q000628:therapy / Q000821:virology*; D003424:Crohn Disease / Q000382:microbiology / Q000473:pathology / Q000628:therapy / Q000821:virology*; D064806:Dysbiosis / Q000382:microbiology / Q000473:pathology / Q000628:therapy / Q000821:virology*; D005243:Feces / Q000382:microbiology / Q000821:virology; D006801:Humans; D054892:Metagenome; D017914:Microviridae / Q000235:genetics / Q000302:isolation & purification*