Evolution of the gut microbiome following acute HIV-1 infection

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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
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
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

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

Curated date: 2022/01/08

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1

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 ControlLinks
Dorea

Revision editor(s): Joyessa, Claregrieve1

Signature 2

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

Curated date: 2022/01/08

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1

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 ControlLinks
Veillonella

Revision editor(s): Joyessa, Claregrieve1