|Year||Technique||Study Groups||Main findings|
|Ellis et al. 2011 ||Kinetic (real time) quantitative-PCR of the 16S rRNA gene||12 HIV positive individuals, 5 seronegative individuals.||
• No significant difference in the total quantity of 16S rRNA gene expression between HIV positive and seronegative individuals.|
• A greater proportion of gram-negative bacteria, order Enterobacteriales was seen in HIV positive individuals compared with seronegative controls.
• The proportions of Enterobacteriales and Bacteroidales correlated with duodenal CD4+ T-cell depletion and peripheral CD8+ T-cell activation, respectively.
|Vujkovic-Cvijin et al. 2013 ||Microarray of 16S rRNA gene||22 HIV positive individuals (6 viremic untreated, 16 on HAART), 9 seronegative individuals||
• Dysbiotic mucosal-adherent microbiota. Enrichment of Proteobacteria and depletion of Bacteroidia in HIV infected individuals.|
• Dysbiosis in individuals on HAART was correlated with the kynurenine pathway of tryptophan catabolism and plasma concentrations of IL-6
|Lozupone et al. 2013 ||V4 region of 16S rRNA gene||22 chronic HIV infected individuals (with or without ART), 3 recently infected HIV positive individuals, 13 HIV seronegative individuals||
• Recently infected individuals have a microbiota that differs only slightly from the microbiota of uninfected individuals.|
• Short-term ART did not restore the microbiota to its uninfected composition.
• Increase abundances of Prevotellaceae, Erysipelotrichaceae, Veillonellaceae, Clostridium cluster XIII and the genus Desulfovibrio in chronically untreated individuals compared to HIV seronegative individuals.
• HIV seronegative individuals had increased abundance of Bacteroidaceae, Rikenellaceae, and Porphyromonadaceae.
|McHardy et al. 2013 ||V4 region of 16S rRNA gene, in-silico metagenomics||20 HIV seronegative individuals, 20 HIV positive individuals on ART, 20 HIV positive individuals not on ART.||
• Depletion of specific genera (such as Lachnospira, and Eubacterium,) and enrichment of other genera (such as Porphyromonas and Anaerococcus) in HIV positive individuals not on ART.|
• HIV positive individuals on ART showed similar trends but to a lesser extent.
• Differences in attributed functionality were found between HIV positive individuals not receiving ART and healthy controls (eg. amino acid metabolism and vitamin biosynthesis).
|Pérez-Santiago et al. 2013 ||V6 region of 16S rRNA gene||13 HIV positive individuals (before and during ART)||
• Enrichment of Lactobacillales in HIV infected individuals before ART was associated with lower viral loads, higher CD4 T cell concentrations and lower markers of microbial translocation.|
• Enrichment of Lactobacillales in HIV infected individuals after ART initiation was associated with lower translocation, lower systemic immune activation and higher CD4 T cell concentrations
|Mutlu et al. 2014 ||16S rRNA gene||21 HIV positive individuals, 22 seronegative individuals.||
• Reduced alpha diversity in the terminal ileum and colon were observed in HIV infection.|
• Bacteria that increased in the HIV positive group are potentially pathogenic in other disease states.
• Higher diversity between microbiota samples in the HIV positive group compared with the seronegative group.
• A significant increase in Brachyspira, Campylobacter, Catenibacterium, Escherichia, Mogibacterium, Prevotella, and Ralstonia was observed in the HIV positive group.
• An increase in Akkermansia, Bacteroides, Blautia, Coprococcus, Dialister, Dorea, Faecalibacterium, Lachnospira, Roseburia, Ruminococcus, Odoribacter, Oscillospira was observed in the seronegative individuals group.
|Lozupone et al. 2014 ||V4 region of 16S rRNA gene||40 HIV positive individuals (of them 28 on ART), 15 HIV seronegative individuals.||
• The microbiota composition of individuals on ART was more similar to that of individuals with untreated HIV infection than seronegative individuals.|
• Bacteroides and Odoribacter genera and Parabacteroides distasonis decrease with HIV infection, remain at low abundances in most individuals on ART.
• Prevotella genus, the Paraprevotellaceae family, and Eubacterium biforme increase with HIV infection, abundance varies in individuals undergoing ART (do not reach typical low levels of HIV-negative individuals).
• Peptococcus genus increased in untreated HIV infected individuals and decreases with ART.
• Desulfovibrio and Catenibacterium genera increase in untreated HIV infected individuals, while in individuals on ART they trended back to levels seen in HIV seronegative individuals.
|Dillon et al. 2014 ||V4 region of 16S rRNA gene||18 untreated HIV positive individuals, 14 seronegative individuals||
• Increased abundance of Proteobacteria and decreased abundance of Firmicutes in colon biopsies of HIV infected individuals compared with seronegative individuals.|
• Within the Proteobacteria phylum, an increase in Brucellaceae, Xanthomonadaceae and Moraxellaceae and a decrease in Rhodospirillaceae was observed in HIV infected individuals.
• Within the Bacteroidetes phylum, an increase in Prevotellaceae and a decrease in Bacteroidaceae, Prophyromonadaceae and Rikenellaceae was observed HIV positive individuals.
• Within the Firmicutes phylum, Lachnospiraceae, Christensenellaceae and Ruminococcaceae were decreased in HIV-infected patients.
• The increased abundance in Proteobacteria seen in mucosal samples of HIV positive individuals, was not observed in fecal aspirates or rectal swabs.
• The decrease in mucosal Firmicutes in HIV infected individuals was observed in fecal aspirates, but not in stool samples.
• Trends seen in mucosal abundances of Proteobacteria and Firmicutes families and genera were not consistent in stool samples and fecal aspirates.
|Nowak et al. 2015 ||V3-V4 region of 16S rRNA gene||31 HIV positive individuals (28 viremic, 3 elite controllers), 9 HIV seronegative individuals||
• Decreased alpha diversity in untreated HIV infected patients.|
• A further decrease in alpha diversity following ART.
• Prevotella genus significantly reduced during ART in HIV positive individuals.
• Higher relative abundance of Bacteroidetes in elite controllers compared to viremic patients.
• Increased abundance of Actinobacteria and Proteobacteria in viremic patients compared to elite controllers.
• Elite controllers did not differ significantly from seronegative controls at the phylum level.
• Increased relative abundance of Lactobacillus in viremic patients compared to seronegative individuals.
• Lachnobacterium, Faecalibacterium, and Haemophilus were significantly reduced in viremic patients compared to seronegative individuals.
|Vázquez-Castellanos et al. 2015 ||V1, V2, V3 regions of 16S rRNA gene, whole genome shotgun sequencing||15 HIV positive individuals on ART, 15 seronegative individuals||
• Healthy subjects cluster separately from positive subjects based on 16S rRNA sequencing.|
• Enrichment in Prevotella and Succinivibrio in the microbiota of HIV positive individuals.
• Seronegative control individuals presented with microbiota enriched with Bacteroides and Faecalibacterium and generally had a more diverse composition.
• 12 KEGG pathways found to be enriched in the HIV positive subjects, specifically “ribosome” and “LPS biosynthesis” pathways being the most discriminative.
• 23 KEGG pathways found to be enriched in seronegative control, “starch and sucrose metabolism” and “glycolysis/gluconeogenesis” being the most discriminative.
|Dinh et al. 2015 ||V3-V5 region of 16S rRNA gene||21 HIV positive individuals on ART, 16 seronegative individuals||
• Greater abundance of Proteobacteria in HIV positive individuals compared to controls.|
• Enrichment in Gammaproteobacteria, Enterobacteriales and Enterobacteriaceae in the Proteobacteria phylum in HIV positive individuals compared to controls.
• Enrichement in Erysipelotrichi, Erysipelotrichales, and Erysipelotrichaceae in the Firmicutes phylum in HIV positive individuals compared to controls.
• Enrichement in Barnesiella and reduction in Rikenellaceae and Alistipes in the phylum Bacteroidetes in HIV positive individuals compared to controls.
|Monaco et al. 2016 ||V4 region of 16S rRNA gene||40 HIV positive individuals on ART, 42 HIV positive individuals not on ART, 40 HIV seronegative individuals||
• Low peripheral CD4 T cell counts associated with reduced phylogenetic diversity and species richness.|
• Low peripheral CD4 T cell concentration associated with an increase in a group of bacteria such as Enterbacteriaceae, Enterococcaceae and Lactobacillaceae.