title: HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria.
abstract: OBJECTIVE
  To evaluate the impact of HIV infection on colonization resistance in the proximal gut.
  
  
  METHODS
  It was a case-control study.
  
  
  METHODS
  We contrasted microbiota composition between eight HIV-1-infected patients and eight HIV-negative controls to characterize community alteration and detect exogenous bacteria in the esophagus, stomach, and duodenum, as well as the mouth using a universal 16s ribosomal RNA gene survey and correlated the findings with HIV serostatus and peripheral blood T-cell counts.
  
  
  RESULTS
  HIV infection was associated with an enrichment of Proteobacteria (P=0.020) and depletion of Firmicutes (P = 0.005) in the proximal gut. In particular, environmental species Burkholderia fungorum and Bradyrhizobium pachyrhizi colonized the duodenum of HIV patients who had abnormal blood CD4 T-cell counts but were absent in HIV-negative controls or HIV patients whose CD4 cell counts were normal. The two species coexisted and exhibited a decreasing trend proximally toward the stomach and esophagus and were virtually absent in the mouth. B. fungorum always outnumbered B. pachyrhizi in a ratio of approximately 15 to 1 regardless of the body sites (P < 0.0001, r = 0.965). Their abundance was inversely correlated with CD4 cell counts (P = 0.004) but not viral load. Overgrowth of potential opportunistic pathogens for example, Prevotella, Fusobacterium, and Ralstonia and depletion of beneficial bacteria, for example, Lactobacillus was also observed in HIV patients.
  
  
  CONCLUSIONS
  The colonization of the duodenum by environmental bacteria reflects loss of colonization resistance in HIV infection. Their correlation with CD4 cell counts suggests that compromised immunity could be responsible for the observed invasion by exogenous microbes.
authors.affiliation: aDepartment of Medicine, New York University School of MedicinebThe Department of Veterans Affairs New York Harbor Healthcare SystemcNew York University School of DentistrydDepartment of Pathology, New York University School of Medicine, New York City, New YorkeGene By Gene, Ltd., Houston, Texas, USA.
authors.forename: Liying
authors.initials: L
authors.lastname: Yang
authors.forename: Michael A
authors.initials: MA
authors.lastname: Poles
authors.forename: Gene S
authors.initials: GS
authors.lastname: Fisch
authors.forename: Yingfei
authors.initials: Y
authors.lastname: Ma
authors.forename: Carlos
authors.initials: C
authors.lastname: Nossa
authors.forename: Joan A
authors.initials: JA
authors.lastname: Phelan
authors.forename: Zhiheng
authors.initials: Z
authors.lastname: Pei
mesh_terms: D000328:Adult; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D058448:Biota; D016022:Case-Control Studies; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D004386:Duodenum / Q000382:microbiology*; D004947:Esophagus / Q000382:microbiology*; D005260:Female; D015658:HIV Infections / Q000276:immunology*; D006801:Humans; D007108:Immune Tolerance; D008297:Male; D008875:Middle Aged; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013270:Stomach / Q000382:microbiology*; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S