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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.