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Metagenomic analysis reveals rectal microbiota features associated with HIV and behavioral factors in Nigerian men who have sex with men
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  • Published: 05 March 2026

Metagenomic analysis reveals rectal microbiota features associated with HIV and behavioral factors in Nigerian men who have sex with men

  • R. G. Nowak1,14 na1,
  • E. Gough2 na1,
  • J. H. Holm3,4,
  • F. Hu5,10,
  • K. Akinyombo6,
  • C. Okudo6,
  • P. J. Ozumba6,
  • E. C. Jonathan6,
  • A. B. Tiamiyu7,8,
  • A. Kokogho7,8,
  • S. B. Adebajo1,6,
  • E. Shoyemi9,
  • S. D. Baral2,
  • K. Lombardi5,10,
  • S. Peel11,
  • J. N. Lim3,12,
  • C. A. Gaydos13,
  • Y. C. Manabe13,
  • C. L. Sears13,
  • M. Shardell3,14,
  • J. Ravel3,4 na1,
  • T. A. Crowell5,10 na1 &
  • …
  • Susan Tuddenham13 na1 

Scientific Reports , Article number:  (2026) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Medical research
  • Microbiology

Abstract

Emerging data suggest unique features characterize the rectal microbiota of men who have sex with men (MSM) and people living with HIV (PLWH). The microbiota may have important health implications in these groups, but most studies have been conducted in the United States or Europe. This study leveraged metagenomic sequencing to evaluate relationships between rectal microbiota composition and clinical, behavioral and demographic characteristics in a cohort of Nigerian MSM. PLWH with suppressed viral load had lower α-diversity (richness) compared to people without HIV (PWoH), with similar trends for PLWH with an unsuppressed viral load. Lower α-diversity (Shannon) was associated with use of petroleum jelly lubricant for anal sex. Lower relative abundance of the genus Prevotella was seen in PLWH with a suppressed viral load versus PWoH. There were differences in abundance of the top 20 taxa associated with age, HIV status (enhanced in virally suppressed PLWH versus PWoH), lubricant use, receptive anal intercourse, and condom use, suggesting multiple clinical and behavioral factors impact the rectal microbiota. Future characterization of health outcomes associated with the rectal or gut microbiota in MSM and PLWH as well as potential interventional insights will necessitate larger, dedicated studies across diverse geographic locations.

Data availability

The data that support the findings of this study are not openly available due to reasons of sensitivity but will be available for research purposes upon reasonable request through request to dbGaP. The dbGaP ID is phs003939.v1.p1.

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Funding

This work was supported in part agreements between the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., and the U.S. Department of Defense [W81XWH-11-2-0174, W81XWH-18-2-0040, HT9425-24-3-0004]; the National Institute of Mental Health (NIMH) and the National Institute of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health under award R01MH099001, R01AI120913, and R21AI156765; and the President’s Emergency Plan for AIDS Relief through a cooperative agreement between the Department of Health and Human Services/Centers for Disease Control and Prevention, Global AIDS Program, and the Institute for Human Virology-Nigeria [NU2GGH002099]. Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the author, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense, the Department of Health and Human Services, the National Institutes of Health, or the Henry M. Jackson Foundation for the Advancement of Military Medicine. The investigators have adhered to the policies for protection of human participants in research as prescribed in AR 70 − 25.

Author information

Author notes

  1. R. G. Nowak, E. Gough, J. Ravel, T. A. Crowell and Susan Tuddenham contributed equally to this work.

Authors and Affiliations

  1. Institute of Human Virology, University of Maryland, Baltimore, MD, USA

    R. G. Nowak & S. B. Adebajo

  2. Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

    E. Gough & S. D. Baral

  3. Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA

    J. H. Holm, J. N. Lim, M. Shardell & J. Ravel

  4. Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, USA

    J. H. Holm & J. Ravel

  5. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA

    F. Hu, K. Lombardi & T. A. Crowell

  6. Institute of Human Virology Nigeria, Abuja, Nigeria

    K. Akinyombo, C. Okudo, P. J. Ozumba, E. C. Jonathan & S. B. Adebajo

  7. U.S. Military HIV Research Program, Walter Reed Army Institute of Research – Africa, Abuja, Nigeria

    A. B. Tiamiyu & A. Kokogho

  8. Henry M. Jackson Foundation Medical Research International, Abuja, Nigeria

    A. B. Tiamiyu & A. Kokogho

  9. Population Council, Lagos, Nigeria

    E. Shoyemi

  10. U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, MD, USA

    F. Hu, K. Lombardi & T. A. Crowell

  11. Diagnostics and Countermeasures Branch, CIDR, Walter Reed Army Institute of Research, Silver Spring, MD, USA

    S. Peel

  12. MD Genomics, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA

    J. N. Lim

  13. Division of Infectious Diseases, Johns Hopkins School of Medicine, 5200 Eastern Ave, MFL Center Tower, Suite 381, Baltimore, MD, 21224, USA

    C. A. Gaydos, Y. C. Manabe, C. L. Sears & Susan Tuddenham

  14. Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA

    R. G. Nowak & M. Shardell

Authors
  1. R. G. Nowak
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  2. E. Gough
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  3. J. H. Holm
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  4. F. Hu
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  5. K. Akinyombo
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  9. A. B. Tiamiyu
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Contributions

Susan Tuddenham, Trevor Crowell, Rebecca Nowak, Cynthia Sears and Jacques Ravel conceived of the study. Susan Tuddenham, Trevor Crowell, Rebecca Nowak, Michelle Shardell, Cynthia Sears, Ethan Gough and Jacques Ravel designed the study. Rebecca Nowak, Trevor Crowell, Fengming Hu, Kehinde Akinyombo, Chinenye Okudo, Petronilla Ozumba, Emmanuel Chukwuemeka Jonathan, Abdulwasiu B Tiamiyu, Afoke Kokogho, Jonathan Lim, Jacques Ravel, Johanna Holm, Elizabeth Shoyemi, Stefan Baral, Kara Lombardi, Sheila Peel, Sylvia Adebajo, Charlotte Gaydos contributed to data collection and generation. Ethan Gough and Fengming Hu cleaned the data and conducted the statistical analysis. All authors including Yuka Manabe contributed significantly to drafting and substantial revision of the work.”

Corresponding author

Correspondence to Susan Tuddenham.

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Competing interests

ST has been a consultant for Biofire Diagnostics, Roche Molecular Diagnostics and Luca Biologics, receives royalties from UpToDate and has received speaker honoraria from Roche Molecular Diagnostics and Medscape/WebMD. She participates in research supported by in-kind donation of test kits from Hologic. CG reports consultations for Rover, Dx Inc; Autonomous Medical Devices, Inc; Binx Health, Inc; and BioMedical Insights. C.L.S. has received research funding to Johns Hopkins University from Bristol-Myers Squibb and Janssen, and royalties from Up to Date outside the submitted work. All the remaining authors declare no conflict of interest.

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Nowak, R.G., Gough, E., Holm, J.H. et al. Metagenomic analysis reveals rectal microbiota features associated with HIV and behavioral factors in Nigerian men who have sex with men. Sci Rep (2026). https://doi.org/10.1038/s41598-026-42119-5

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  • Received: 10 June 2025

  • Accepted: 24 February 2026

  • Published: 05 March 2026

  • DOI: https://doi.org/10.1038/s41598-026-42119-5

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