Evolution of the gut microbiome following acute HIV-1 infection

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

31078141

DOI Digital object identifier for electronic documents.

10.1186/s40168-019-0687-5

URI

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511141/pdf/40168_2019_Article_687.pdf

Authors

Rocafort M, Noguera-Julian M, Rivera J, Pastor L, Guillén Y, Langhorst J, Parera M, Mandomando I, Carrillo J, Urrea V, Rodríguez C, Casadellà M, Calle ML, Clotet B, Blanco J, Naniche D, Paredes R

Journal

Microbiome

Year

2019

Keywords:

AIDS, HIV-1, HIV-1 pathogenesis, Microbiome, acute HIV-1 infection

BACKGROUND: In rhesus macaques, simian immunodeficiency virus infection is followed by expansion of enteric viruses but has a limited impact on the gut bacteriome. To understand the longitudinal effects of HIV-1 infection on the human gut microbiota, we prospectively followed 49 Mozambican subjects diagnosed with recent HIV-1 infection (RHI) and 54 HIV-1-negative controls for 9-18 months and compared them with 98 chronically HIV-1-infected subjects treated with antiretrovirals (n = 27) or not (n = 71). RESULTS: We show that RHI is followed by increased fecal adenovirus shedding, which persists during chronic HIV-1 infection and does not resolve with ART. Recent HIV-1 infection is also followed by transient non-HIV-specific changes in the gut bacterial richness and composition. Despite early resilience to change, an HIV-1-specific signature in the gut bacteriome-featuring depletion of Akkermansia, Anaerovibrio, Bifidobacterium, and Clostridium-previously associated with chronic inflammation, CD8+ T cell anergy, and metabolic disorders, can be eventually identified in chronically HIV-1-infected subjects. CONCLUSIONS: Recent HIV-1 infection is associated with increased fecal shedding of eukaryotic viruses, transient loss of bacterial taxonomic richness, and long-term reductions in microbial gene richness. An HIV-1-associated microbiome signature only becomes evident in chronically HIV-1-infected subjects.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31

Curated date: 2022/01/08

Curator: Joyessa

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Joyessa

Subjects

Location of subjects: Mozambique

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HIV-1-negative individuals

Group 1 name Corresponds to the case (exposed) group for case-control studies: Recently HIV-1 infected individuals

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Individuals with recent HIV infection (RHI), defined as a negative or indeterminate rapid test serology (first test negative or first test positive and second test negative) and positive HIV-1 viremia

Group 0 sample size Number of subjects in the control (unexposed) group: 54

Group 1 sample size Number of subjects in the case (exposed) group: 49

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

Statistical test: Kruskall-Wallis

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

Matched on Factors on which subjects have been matched on in a case-control study: age, body mass index

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Richness Number of species: increased

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31

Curated date: 2022/01/08

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1, WikiWorks

Source: Figure 2

Description: Differential microbial abundance between recently HIV-1 infected and HIV-negative individuals

Abundance in Group 1: decreased abundance in Recently HIV-1 infected individuals

NCBI	Quality Control	Links
Dorea

Revision editor(s): Joyessa, Claregrieve1, WikiWorks

Signature 2

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Your review change was submitted

Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31

Curated date: 2022/01/08

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1, WikiWorks

Source: Figure 2

Description: Differential microbial abundance between recently HIV-1 infected and HIV-negative individuals

Abundance in Group 1: increased abundance in Recently HIV-1 infected individuals

NCBI	Quality Control	Links
Veillonella

Revision editor(s): Joyessa, Claregrieve1, WikiWorks