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Table 1 Summarizing Microbiota in HIV Table

From: The gut microbiome in human immunodeficiency virus infection

Year Technique Study Groups Main findings
Ellis et al. 2011 [33] 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 [32] 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 [27] 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 [39] 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 [35] 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 [29] 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 [24] 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 [28] 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 [26] 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 [37] 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 [23] 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 [36] 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.