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. Author manuscript; available in PMC: 2017 Jun 1.
Published in final edited form as: Clin Pharmacol Ther. 2016 Apr 16;99(6):600–611. doi: 10.1002/cpt.363

Table 1.

Summary of HIV microbiome studies.

Study Study location N of HIV+ group (male/female) Type of sample evaluated Serum CD4+ T cells (cells/ul) ART Summary of observed dysbiosis (HIV+ vs controls)
Lozupone et al 2013, 2014 Denver, USA Untreated: 11/0
Treated: 7/1		 Feces Untreated: 551 (270–1095)
Treated: 483 (204–876)		 Both +/− Untreated:
Inline graphic Bacteroides
Inline graphic Prevotella
Inline graphic alpha-diversity
Treated:
Inline graphic Bacteroides
Inline graphic Prevotella
McHardy et al 2013 Los Angeles, USA Untreated: 20/0
Treated: 20/0		 Anal washes Untreated: 439 (271 SD)
Treated: 534 (246 SD)		 Both +/− Untreated:
Inline graphic Coprococcus
Inline graphic Alistipes
Inline graphic Fusobacteria
Inline graphic alpha-diversity
Treated:
Intermediate dysbiosis
Vujkovic-Cvijin 2013 San Francisco, USA Untreated: 6/0
Treated: 16/0		 Colon Untreated: 356 (313–819)
Treated: 374 (251–1110)		 Both +/− Untreated:
Inline graphic Bacteroides
Inline graphic Pathogenic spp.
Treated:
Intermediate dysbiosis
Dillon et al 2014 Denver, USA 13/5 Feces, colon 425 (238–782) Untreated Inline graphic Bacteroides
Inline graphic Prevotella
Inline graphic Proteobacteria
Mucosa only:
Inline graphic alpha-diversity
Mutlu et al 2014 Chicago, USA 16/5 Feces, colon, ileum 425 (106–948) Treated Inline graphic Bacteroides
Inline graphic Prevotella
Inline graphic Proteobacteria
Inline graphic alpha-diversity
Vasquez-Castellanos et al 2014 Madrid, Spain 12/3 Feces 584 (466–794 range) Treated Inline graphic Bacteroides
Inline graphic Prevotella
Inline graphic Coprococcus
Yu et al 2014 Washington, DC and New York City, USA 76/0 Anal swab Swab 1: 580 (432–721)
Swab 2: 232 (32–415)		 NRTI only, no combined therapy Baseline:
Inline graphic Fusobacteria
Inline graphic Firmicutes
Follow-up 1–5 yrs:
Inline graphic Fusobacteria
Inline graphic alpha-diversity
Dinh et al 2015 Boston, USA 17/4 Feces 668 (424–870) Treated Inline graphic Alistipes
Inline graphic Barnsiella
Inline graphic Proteobacteria
Nowak et al 2015 Stockholm, Sweden 16/15 Feces Before treatment:
355 (120–2470)		 Both +/− (longitudinal) Before ART:
Inline graphic Lachnobacterium
Inline graphic Lactobacillus
Inline graphic alpha-diversity
Following ART:
Inline graphicPrevotella
Inline graphic alpha-diversity
Yang et al 2016 New York City, USA 5/3 Duodenum, proximal gut 327 (12–708) Untreated Inline graphic Lactobacillus
Inline graphic Proteobacteria
Inline graphic Firmicutes
Low CD4 count:
Inline graphic Burkholderia
Noguera-Julian et al 2016 Barcelona, Spain and Stockholm, Sweden Barcelona: 101/28 (15 untreated)
Stockholm: 46/31 (all untreated)		 Feces 700 (462–860 IQR) Both +/− Inline graphic alpha-diversity
Unique findings: Prevotella/Bacteroides abundance associated with sexual behavior

Inline graphic: increase, Inline graphic: decrease; for CD4+ T cell count, numbers correspond to either mean or median (with either range, SD=standard deviation, or IQR=interquartile range); for ART, “+” corresponds to treated and “−” corresponds to untreated; NRTI = non-nucleoside reverse transcriptase inhibitor