title: A compositional look at the human gastrointestinal microbiome and immune activation parameters in HIV infected subjects.
abstract: HIV progression is characterized by immune activation and microbial translocation. One factor that may be contributing to HIV progression could be a dysbiotic microbiome. We therefore hypothesized that the GI mucosal microbiome is altered in HIV patients and this alteration correlates with immune activation in HIV. 121 specimens were collected from 21 HIV positive and 22 control human subjects during colonoscopy. The composition of the lower gastrointestinal tract mucosal and luminal bacterial microbiome was characterized using 16S rDNA pyrosequencing and was correlated to clinical parameters as well as immune activation and circulating bacterial products in HIV patients on ART. The composition of the HIV microbiome was significantly different than that of controls; it was less diverse in the right colon and terminal ileum, and was characterized by loss of bacterial taxa that are typically considered commensals. In HIV samples, there was a gain of some pathogenic bacterial taxa. This is the first report characterizing the terminal ileal and colonic mucosal microbiome in HIV patients with next generation sequencing. Limitations include use of HIV-infected subjects on HAART therapy.
authors.affiliation: Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Ece A
authors.initials: EA
authors.lastname: Mutlu
authors.affiliation: Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America ; Department of Pharmacology, The Graduate College, Rush University, Chicago, Illinois, United States of America ; Department of Physiology and Molecular Biophysics, Rush University Medical Center, Chicago, Illinois, United States of America ; Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
authors.forename: Ali
authors.initials: A
authors.lastname: Keshavarzian
authors.affiliation: Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: John
authors.initials: J
authors.lastname: Losurdo
authors.affiliation: Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Garth
authors.initials: G
authors.lastname: Swanson
authors.affiliation: Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Basile
authors.initials: B
authors.lastname: Siewe
authors.affiliation: Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America ; Department of Biochemistry, The Graduate College, Rush University, Chicago, Illinois, United States of America.
authors.forename: Christopher
authors.initials: C
authors.lastname: Forsyth
authors.affiliation: Ruth M. Rothstein CORE Center/Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Audrey
authors.initials: A
authors.lastname: French
authors.affiliation: Ruth M. Rothstein CORE Center/Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Patricia
authors.initials: P
authors.lastname: Demarais
authors.affiliation: Research and Testing Laboratory, LLC., Lubbock, Texas, United States of America.
authors.forename: Yan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Research and Testing Laboratory, LLC., Lubbock, Texas, United States of America.
authors.forename: Lars
authors.initials: L
authors.lastname: Koenig
authors.affiliation: Research and Testing Laboratory, LLC., Lubbock, Texas, United States of America.
authors.forename: Stephen
authors.initials: S
authors.lastname: Cox
authors.affiliation: Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Phillip
authors.initials: P
authors.lastname: Engen
authors.affiliation: Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Prachi
authors.initials: P
authors.lastname: Chakradeo
authors.affiliation: Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Rawan
authors.initials: R
authors.lastname: Abbasi
authors.affiliation: Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Annika
authors.initials: A
authors.lastname: Gorenz
authors.affiliation: Rush Medical College, Armour Academic Center, Chicago, Illinois, United States of America.
authors.forename: Charles
authors.initials: C
authors.lastname: Burns
authors.affiliation: Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands ; Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America.
authors.forename: Alan
authors.initials: A
authors.lastname: Landay
mesh_terms: D005260:Female; D015658:HIV Infections / Q000276:immunology* / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007413:Intestinal Mucosa / Q000276:immunology* / Q000382:microbiology*; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D012336:RNA, Ribosomal, 16S / Q000032:analysis*; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D012336:RNA, Ribosomal, 16S