title: Anal microbiota profiles in HIV-positive and HIV-negative MSM.
abstract: OBJECTIVE
  Because differences in anal microbial populations (microbiota) could affect acquisition of HIV or other conditions, especially among MSM, we profiled the microbiota of the anal canal, assessed its stability, and investigated associations with diversity and composition.
  
  
  METHODS
  Microbiota profiles in anal swabs collected from 76 MSM (52 in 1989, swab-1; 66 1-5 years later, swab-2) were compared by HIV status (25 HIV-positive), T-cell subsets, and questionnaire data.
  
  
  METHODS
  Bacterial 16S rRNA genes were amplified, sequenced (Illumina MiSeq), and clustered into species-level operational taxonomic units (QIIME and Greengenes). Regression models and Wilcoxon tests were used for associations with alpha diversity (unique operational taxonomic units, Shannon's index). Composition was compared by Adonis (QIIME).
  
  
  RESULTS
  Most anal bacteria were Firmicutes (mean 60.6%, range 21.1-91.1%) or Bacteroidetes (29.4%, 4.1-70.8%). Alpha diversity did not change between the two swabs (N = 42 pairs). In swab-2, HIV-positives had lower alpha diversity (P ≤ 0.04) and altered composition, with fewer Firmicutes and more Fusobacteria taxa (P ≤ 0.03), not completely attributable to very low CD4(+) cell count (median 232 cells/μl), prior AIDS clinical diagnosis (N = 17), or trimethoprim-sulfamethoxazole use (N = 6). Similar but weaker differences were observed in swab-1 (HIV-positive median 580 CD4(+) cells/μl; no trimethoprim-sulfamethoxazole). Associations with T-cell subsets, smoking, and sexual practices were null or inconsistent.
  
  
  CONCLUSIONS
  The anal microbiota of MSM was relatively stable over 1-5 years. However, with uncontrolled, advanced HIV infection, the microbiota had altered composition and reduced diversity partially attributable to antibiotics. Investigations of microbial community associations with other immune perturbations and clinical abnormalities are needed.
authors: aInfections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda bInstitute of Genomic Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.
authors: Guoqin
authors: G
authors: Yu
authors: Doug
authors: D
authors: Fadrosh
authors: Bing
authors: B
authors: Ma
authors: Jacques
authors: J
authors: Ravel
authors: James J
authors: JJ
authors: Goedert
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000473:pathology*; D000328:Adult; D000368:Aged; D001003:Anal Canal / Q000382:microbiology*; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D058448:Biota; D018791:CD4 Lymphocyte Count; D016000:Cluster Analysis; D015331:Cohort Studies; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D018451:Homosexuality, Male; D006801:Humans; D008297:Male; D008875:Middle Aged; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013997:Time Factors
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S