title: The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis.
abstract: The vertebrate gut harbors a vast community of bacterial mutualists, the composition of which is modulated by the host immune system. Many gastrointestinal (GI) diseases are expected to be associated with disruptions of host-bacterial interactions, but relatively few comprehensive studies have been reported. We have used the rhesus macaque model to investigate forces shaping GI bacterial communities. We used DNA bar coding and pyrosequencing to characterize 141,000 sequences of 16S rRNA genes obtained from 100 uncultured GI bacterial samples, allowing quantitative analysis of community composition in health and disease. Microbial communities of macaques were distinct from those of mice and humans in both abundance and types of taxa present. The macaque communities differed among samples from intestinal mucosa, colonic contents, and stool, paralleling studies of humans. Communities also differed among animals, over time within individual animals, and between males and females. To investigate changes associated with disease, samples of colonic contents taken at necropsy were compared between healthy animals and animals with colitis and undergoing antibiotic therapy. Communities from diseased and healthy animals also differed significantly in composition. This work provides comprehensive data and improved methods for studying the role of commensal microbiota in macaque models of GI diseases and provides a model for the large-scale screening of the human gut microbiome.
authors.affiliation: Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.
authors.forename: Philip
authors.initials: P
authors.lastname: McKenna
authors.forename: Christian
authors.initials: C
authors.lastname: Hoffmann
authors.forename: Nana
authors.initials: N
authors.lastname: Minkah
authors.forename: Pyone Pyone
authors.initials: PP
authors.lastname: Aye
authors.forename: Andrew
authors.initials: A
authors.lastname: Lackner
authors.forename: Zongzhi
authors.initials: Z
authors.lastname: Liu
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Lozupone
authors.forename: Micah
authors.initials: M
authors.lastname: Hamady
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.forename: Frederic D
authors.initials: FD
authors.lastname: Bushman
mesh_terms: D000818:Animals; D001419:Bacteria / Q000302:isolation & purification; D001483:Base Sequence; D002908:Chronic Disease; D003106:Colon / Q000382:microbiology*; D004269:DNA, Bacterial / Q000032:analysis; D004195:Disease Models, Animal; D004760:Enterocolitis / Q000382:microbiology* / Q000503:physiopathology; D054884:Host-Pathogen Interactions; D016180:Lentivirus Infections / Q000382:microbiology* / Q000503:physiopathology; D017958:Lentiviruses, Primate / Q000302:isolation & purification / Q000502:physiology; D008253:Macaca mulatta / Q000382:microbiology*; D054892:Metagenome; D008969:Molecular Sequence Data; D008992:Monkey Diseases / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S