Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-12-18

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

33828220

DOI Digital object identifier for electronic documents.

10.1038/s41598-021-87368-8

URI

https://doi.org/10.1038/s41598-021-87368-8

Authors

Abange WB, Martin C, Nanfack AJ, Yatchou LG, Nusbacher N, Nguedia CA, Kamga HG, Fokam J, Kennedy SP, Ndjolo A, Lozupone C, Nkenfou CN

Journal

Scientific reports

Year

2021

Multiple factors, such as immune disruption, prophylactic co-trimoxazole, and antiretroviral therapy, may influence the structure and function of the gut microbiome of children infected with HIV from birth. In order to understand whether HIV infection altered gut microbiome and to relate changes in microbiome structure and function to immune status, virological response and pediatric ART regimens, we characterized the gut microbiome of 87 HIV-infected and 82 non-exposed HIV-negative children from Yaounde, a cosmopolitan city in Cameroon. We found that children living with HIV had significantly lower alpha diversity in their gut microbiome and altered beta diversity that may not be related to CD4+ T cell count or viral load. There was an increased level of Akkermansia and Faecalibacterium genera and decreased level of Escherichia and other Gamma proteobacteria in children infected with HIV, among other differences. We noted an effect of ethnicity/geography on observed gut microbiome composition and that children on ritonavir-boosted protease inhibitor (PI/r)-based ART had gut microbiome composition that diverged more from HIV-negative controls compared to those on non-nucleoside reverse-transcriptase inhibitors-based ART. Further studies investigating the role of this altered gut microbiome in increased disease susceptibility are warranted for individuals who acquired HIV via mother-to-child transmission.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-18

Curated date: 2024/10/29

Curator: ToluwalaseA

Revision editor(s): ToluwalaseA, Aleru Divine

Subjects

Location of subjects: Cameroon

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: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: HIV infection [X]Human immunodeficiency virus disease,[X]Human immunodeficiency virus disease (disorder),[X]Unspecified human immunodeficiency virus [HIV] disease,[X]Unspecified human immunodeficiency virus [HIV] disease (disorder),HIV - Human immunodeficiency virus infection,HIV INFECT,HIV Infection,HIV infection,HIV Infections,HIV infectious disease,HTLV III INFECT,HTLV III Infections,HTLV III LAV INFECT,HTLV III LAV Infections,HTLV WIII INFECTIONS,HTLV WIII LAV INFECTIONS,HTLV-III Infection,HTLV-III Infections,HTLV-III-LAV Infection,HTLV-III-LAV Infections,HUMAN IMMUNO VIRUS DIS,human immunodeficiency virus,Human immunodeficiency virus [HIV] disease,HUMAN IMMUNOdeficiency VIRUS [HIV] INFECTION,Human immunodeficiency virus caused disease or disorder,Human immunodeficiency virus disease,Human immunodeficiency virus disease (disorder),Human immunodeficiency virus disease or disorder,Human immunodeficiency virus infection,Human immunodeficiency virus infection (disorder),Human immunodeficiency virus infection, NOS,Human immunodeficiency virus infectious disease,human immunodeficiency virus infectious disease,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,LYMPHOTROPIC VIRUS TYPE III INFECTIONS HUMAN T,T LYMPHOTROPIC VIRUS TYPE III INFECT HUMAN,T Lymphotropic Virus Type III Infections, Human,T-Lymphotropic Virus Type III Infections, Human,Unspecified human immunodeficiency virus [HIV] disease (disorder),hIV infection

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Human Immunodeficiency Virus (HIV)-negative children

Group 1 name Corresponds to the case (exposed) group for case-control studies: Human Immunodeficiency Virus (HIV)-positive children

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children diagnosed with HIV and undergoing treatment with either non-nucleoside reverse transcriptase inhibitors (NNRTI) or protease inhibitor (PI/r)-based anti-retroviral therapy (ART).

Group 0 sample size Number of subjects in the control (unexposed) group: 82

Group 1 sample size Number of subjects in the case (exposed) group: 87

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 4 weeks

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: 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)?: Yes

Alpha Diversity

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

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Curated date: 2024/11/07

Curator: ToluwalaseA

Revision editor(s): ToluwalaseA, Aleru Divine

Source: Figure 4A

Description: Differential abundance of ASVs in the HIV-infected and HIV-uninfected cohorts identified via paired, Wilcoxon tests.

Abundance in Group 1: increased abundance in Human Immunodeficiency Virus (HIV)-positive children

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Akkermansia muciniphila

Revision editor(s): ToluwalaseA, Aleru Divine

Signature 2

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Curated date: 2024/11/07

Curator: ToluwalaseA

Revision editor(s): ToluwalaseA, Aleru Divine

Source: Figure 4A

Description: Differential abundance of ASVs in the HIV-infected and HIV-uninfected cohorts identified via paired, Wilcoxon tests.

Abundance in Group 1: decreased abundance in Human Immunodeficiency Virus (HIV)-positive children

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Faecalibacterium prausnitzii

Revision editor(s): ToluwalaseA, Aleru Divine

Experiment 2

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Curated date: 2024/11/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Response to antiviral drug Response to antiviral drug,response to antiviral drug

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-nucleoside reverse transcriptase inhibitors (NNRTI) - based ART

Group 1 name Corresponds to the case (exposed) group for case-control studies: Protease inhibitor (PI/r) - based ART

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children diagnosed with HIV and undergoing treatment with protease inhibitor (PI/r)-based anti-retroviral therapy (ART).

Group 0 sample size Number of subjects in the control (unexposed) group: 74

Group 1 sample size Number of subjects in the case (exposed) group: 13

Lab analysis

Statistical Analysis

Alpha Diversity

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

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Curated date: 2024/11/12

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6A

Description: Differential abundance of ASVs in the HIV-positive NNRTI and PI/r cohorts identified via paired, Wilcoxon tests.

Abundance in Group 1: decreased abundance in Protease inhibitor (PI/r) - based ART

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Blautia
Prevotella
Oscillospira
Faecalibacterium

Revision editor(s): Aleru Divine