Rectal microbiota among HIV-uninfected, untreated HIV, and treated HIV-infected in Nigeria

Study information

Reviewed Marked as Reviewed by Folakunmi on 2024-2-27

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

28118207

DOI Digital object identifier for electronic documents.

10.1097/QAD.0000000000001409

URI

Authors

Nowak RG, Bentzen SM, Ravel J, Crowell TA, Dauda W, Ma B, Liu H, Blattner WA, Baral SD, Charurat ME

Journal

AIDS (London, England)

Year

2017

OBJECTIVE: Untreated advanced HIV infection alters the gut microbiota, but it is unclear whether antiretroviral therapy (ART) reverses these changes. We compared the composition of the rectal microbiota among three groups of men who have sex with men (MSM): HIV-uninfected, untreated HIV, and ART-treated HIV-infected. DESIGN: A cross-sectional study was conducted among 130 MSM (55 HIV-uninfected, 41 untreated HIV, and 34 ART-treated HIV) in Abuja, Nigeria. METHODS: Bacterial 16S rRNA genes were amplified from rectal swabs, sequenced and clustered into Genera-level operational taxonomic units. Alpha diversity was quantified using the Shannon index and compared among groups using the Kruskal-Wallis test; associations with other scale variables were quantified using Spearman's rank correlation (Rs). The relative abundance of the top 15 taxa was compared according to HIV infection/treatment status using the Wilcoxon rank sum test. RESULTS: HIV-treated MSM had a decrease in a commensal phylum, Bacteroidetes (P < 0.01). Alpha diversity was positively correlated with viral loads (Rs = 0.32, P < 0.01). Statistically significant shifts in relative abundance of rectal microbiota for the HIV-treated group included a decrease in the most abundant bacteria, Prevotella (P = 0.02) and an increase in pathogenic bacteria, Peptoniphilus (P = 0.04), Finegoldia (P = 0.01), Anaerococcus (P = 0.03), and Campylobacter (P = 0.03) compared with the other groups. CONCLUSION: Untreated HIV infection does not significantly alter the rectal microbiota, whereas prior treatment is associated with a shift toward a more pathogenic pattern of microbiota. Treatment with an antibiotic, co-trimoxazole, in conjunction with ART may have contributed to this shift.

Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-27

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, LGeistlinger, Victoria

Subjects

Location of subjects: Nigeria

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Rectum

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HIV-uninfected MSM

Group 1 name Corresponds to the case (exposed) group for case-control studies: ART-treated HIV infected MSM

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Men who have sex with men (MSM) with HIV that has been treated with antiretroviral therapy (ART)

Group 0 sample size Number of subjects in the control (unexposed) group: 55

Group 1 sample size Number of subjects in the case (exposed) group: 34

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

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Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): WikiWorks, Folakunmi

Source: Table 1

Description: Relative abundance of most common rectal genera within 5 phyla, stratified by HIV and ART status

Abundance in Group 1: increased abundance in ART-treated HIV infected MSM

NCBI	Quality Control	Links
Anaerococcus
Campylobacter
Finegoldia
Peptoniphilus

Revision editor(s): WikiWorks, Folakunmi

Signature 2

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): WikiWorks, Folakunmi

Source: Table 1

Description: Relative abundance of most common rectal genera within 5 phyla, stratified by HIV and ART status

Abundance in Group 1: decreased abundance in ART-treated HIV infected MSM

NCBI	Quality Control	Links
Prevotella

Revision editor(s): WikiWorks, Folakunmi