title: Fecal bacterial microbiome diversity in chronic HIV-infected patients in China.
abstract: The purpose of this study was to identify fecal bacterial microbiome changes in patients with chronic human immunodeficiency virus (HIV) infection in China. Bacterial 16S rRNA genes were amplified, sequenced (454 pyrosequencing), and clustered into operational taxonomic units using the QIIME software. Relative abundance at the phylum and genus levels were calculated. Alpha diversity was determined by Chao 1 and observed-species indices, and beta diversity was determined by double principal component analysis using the estimated phylogeny-based unweighted Unifrac distance matrices. Fecal samples of the patients with chronic HIV-infection tended to be enriched with bacteria of the phyla Firmicutes (47.20% ± 0.43 relative abundance) and Proteobacteria (37.21% ± 0.36) compared with those of the non-HIV infected controls (17.95% ± 0.06 and 3.81% ± 0.02, respectively). Members of the genus Bilophila were exclusively detected in samples of the non-HIV infected controls. Bacteroides and arabacteroides were more abundant in the chronic HIV-infected patients. Our study indicated that chronic HIV-infected patients in China have a fecal bacterial microbiome composition that is largely different from that found in non-HIV infected controls, and further study is needed to evaluate whether microbiome changes play a role in disease complications in the distal gut, including opportunistic infections.
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.|Department of Laboratory Medicine, Shanghai Guanhua Hospital, Shanghai 200065, China.|Shanghai TargetDrug Ltd., Shanghai 201202, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
authors.forename: Yingfei
authors.initials: Y
authors.lastname: Ma
authors.affiliation: Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200065, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Lin
authors.affiliation: Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Yi-Wei
authors.identifier: http://orcid.org/0000-0003-4888-6771
authors.initials: YW
authors.lastname: Tang
authors.affiliation: Departments of Pathology and Medicine, New York University School of Medicine, New York, NY 10016, USA.|The Department of Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA.
authors.forename: Liying
authors.initials: L
authors.lastname: Yang
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Yinzhong
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Renfan
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Li
authors.initials: L
authors.lastname: Liu
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Jiashen
authors.initials: J
authors.lastname: Shao
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Tangkai
authors.initials: T
authors.lastname: Qi
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Rentian
authors.initials: R
authors.lastname: Cai
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Liqian
authors.initials: L
authors.lastname: Guan
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Luo
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Meiyan
authors.initials: M
authors.lastname: Sun
authors.affiliation: Shanghai TargetDrug Ltd., Shanghai 201202, China.
authors.forename: Ben
authors.initials: B
authors.lastname: Li
authors.affiliation: Departments of Pathology and Medicine, New York University School of Medicine, New York, NY 10016, USA.|The Department of Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA.
authors.forename: Zhiheng
authors.initials: Z
authors.lastname: Pei
authors.affiliation: Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
authors.forename: Hongzhou
authors.initials: H
authors.lastname: Lu
mesh_terms: D000328:Adult; D000368:Aged; D023241:Antiretroviral Therapy, Highly Active; D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D001439:Bacteroides / Q000235:genetics / Q000302:isolation & purification; D001483:Base Sequence; D002681:China / Q000453:epidemiology; D002908:Chronic Disease; D004269:DNA, Bacterial / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D005260:Female; D000068536:Bacillota / Q000235:genetics / Q000302:isolation & purification; D041981:Gastrointestinal Tract / Q000382:microbiology; D014644:Genetic Variation; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology / Q000382:microbiology* / Q000821:virology; D006801:Humans; D064307:Microbiota / Q000235:genetics; D008875:Middle Aged; D010802:Phylogeny; D020560:Proteobacteria / Q000235:genetics / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S