Evidence map›Paper›PMID 41168431›Full record

ArticleNature microbiology2025

Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.

Karolina S Jabbar, Sambhawa Priya, Jiawu Xu, Upasana Das Adhikari, Gleb Pishchany, Ahmed T M Mohamed, Joachim Johansen, Kumar Thurimella, Cristin McCabe, Hera Vlamakis and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors.

Karolina S JabbarBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Sambhawa PriyaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Jiawu XuRagon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-0424-0736
Upasana Das AdhikariRagon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA.
Gleb PishchanyBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Ahmed T M MohamedBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-2390-2210
Joachim JohansenBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Kumar ThurimellaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Cristin McCabeBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Hera VlamakisBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Samson OkelloMbarara University of Science and Technology, Mbarara, Uganda.
Toni M DeloreyBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6614-3803
Alexander LankowskiVaccine & Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-4769-7242
Mosepele MosepeleFaculty of Medicine, University of Botswana, Gaborone, Botswana.
Mark J SiednerMbarara University of Science and Technology, Mbarara, Uganda.
Damian R PlichtaBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6555-2557
Douglas S KwonRagon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA. dkwon@mgh.harvard.edu.ORCID http://orcid.org/0000-0001-8521-8735
Ramnik J XavierBroad Institute of MIT and Harvard, Cambridge, MA, USA. xavier@molbio.mgh.harvard.edu.ORCID http://orcid.org/0000-0002-5630-5167

Funding

Pilot & Feasibility ProgramP30DK043351 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI Ramnik J Xavier · 1991 to 2026
$35.3M
Multi-omics characterization of HIV-associated changes in the gut microbiome and host mucosal immunityR01DK120485 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI KWON, DOUGLAS, XAVIER, RAMNIK J · 2018 to 2022
$4.1M
The enteric microbiome in treated and progressive HIV infectionR01DK101354 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI KWON, DOUGLAS, VIRGIN, HERBERT W · 2014 to 2018
$3.7M
Epidemiology of coronary artery disease among people with HIV in rural sub-Saharan AfricaR01HL141053 · NHLBI · MASSACHUSETTS GENERAL HOSPITAL · PI SIEDNER, MARK J · 2018 to 2021
$3.0M
The enteric microbiome in HIV-associated chronic immune activation and cardiovascular diseaseR01HL138646 · NHLBI · MASSACHUSETTS GENERAL HOSPITAL · PI HANDLEY, SCOTT A., KWON, DOUGLAS · 2017 to 2020
$2.1M
Mentoring patient-oriented research to improve cardiovascular health among people with HIV in sub-Saharan AfricaK24HL166024 · NHLBI · MASSACHUSETTS GENERAL HOSPITAL · PI MARK J SIEDNER · 2022 to 2026
$616k
Epidemiology of atherosclerosis among older-age individuals with HIV in UgandaR21HL124712 · NHLBI · MASSACHUSETTS GENERAL HOSPITAL · PI SIEDNER, MARK J · 2014 to 2015
$332k
NHLBI NIH HHS K24 HL166024NHLBI NIH HHS R01 HL138646NHLBI NIH HHS R01 HL141053NHLBI NIH HHS R21 HL124712NIDDK NIH HHS P30 DK043351NIDDK NIH HHS R01 DK101354NIDDK NIH HHS R01 DK120485U.S. Department of Health & Human Services | National Institutes of Health (NIH) DK120485
6 · The paper itself

Abstract

Human immunodeficiency virus (HIV) infection alters gut microbiota composition and function, but the impact of geography and antiretroviral therapy remains unclear. Here we determined gut microbiome alterations linked to HIV infection and antiretroviral treatment in 327 individuals with HIV and 260 control participants in cohorts from Uganda, Botswana and the USA via faecal metagenomics. We found that while HIV-associated taxonomic differences were mostly site specific, changes in microbial functional pathways were broadly consistent across the cohorts and exacerbated in individuals with acquired immunodeficiency syndrome. Microbiome perturbations associated with antiretroviral medications were also geography dependent. In Botswana and Uganda, use of the non-nucleoside reverse transcriptase inhibitor efavirenz was linked to depletion of Prevotella, disruption of interspecies metabolic networks, exacerbation of systemic inflammation and atherosclerosis. Efavirenz-associated Prevotella depletion may occur through cross-inhibition of prokaryotic reverse transcriptases involved in antiphage defences, as shown by computational and in vitro experiments. These observations could inform future geography-specific and microbiome-guided therapy.

Indexed as

Anti-HIV AgentsAnti-Retroviral AgentsGastrointestinal MicrobiomeHIV InfectionsAdultAlkynesBacteriaBenzoxazinesBotswanaCyclopropanesFecesFemaleHumansMaleMetagenomicsMiddle AgedAlkynesAnti-HIV AgentsAnti-Retroviral AgentsBenzoxazinesCyclopropanesefavirenzReverse Transcriptase Inhibitors

Identifiers

PMID41168431
PMCPMC13188066

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.