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Impact of doxycycline pre-exposure prophylaxis (doxyPrEP) for sexually transmitted infections on the microbiome of men who have sex with men on HIV PrEP

Author

Listed:
  • Samantha Knodel

    (Case Western Reserve University
    University of Manitoba)

  • Leighanne Main

    (Case Western Reserve University)

  • Marlon DeLeon

    (University of Manitoba)

  • Alana Lamont

    (University of Manitoba)

  • Joshua Edward

    (BC Centre for Disease Control
    Nova Scotia Health)

  • Amit K. Gupta

    (BC Centre for Disease Control)

  • Laura Noel-Romas

    (University of Manitoba)

  • Saira Mohammed

    (BC Centre for Disease Control
    BC Centre for Excellence in HIV/AIDS)

  • Tessa Tattersall

    (BC Centre for Disease Control)

  • Jason Wong

    (BC Centre for Disease Control
    University of British Columbia)

  • Mark Hull

    (BC Centre for Excellence in HIV/AIDS
    University of British Columbia
    CIHR Canadian HIV Trials Network)

  • Troy Grennan

    (BC Centre for Excellence in HIV/AIDS
    University of British Columbia
    CIHR Canadian HIV Trials Network)

  • Adam D. Burgener

    (Case Western Reserve University
    University of Manitoba
    Karolinska University Hospital)

Abstract

Doxycycline pre-exposure prophylaxis (doxyPrEP) has shown potential in preventing bacterial sexually transmitted infections, but the impact on the microbiome is unknown. This study assessed rectal microbiome changes over 48 weeks in 41 participants on HIV PrEP (tenofovir disoproxil fumarate/emtricitabine) enrolled in an open-label, randomized pilot trial comparing immediate (100 mg PO daily started immediately and continued to week 48) versus deferred doxyPrEP (100 mg PO daily starting at week 24, continued to week 48) in HIV-negative gay and bisexual men (Clinical Trial #: NCT02844634). Primary study outcomes included feasibility, adherence, and tolerability of the dual PrEP regimen, while exploratory outcomes included rectal microbiome changes. We performed 16S rRNA sequencing from participants that collected baseline, week 24, and week 48 samples. Microbial composition did not significantly change over time in either study arm as measured by individual taxa levels, or alpha and beta diversity at the genus level. A slight decrease (

Suggested Citation

  • Samantha Knodel & Leighanne Main & Marlon DeLeon & Alana Lamont & Joshua Edward & Amit K. Gupta & Laura Noel-Romas & Saira Mohammed & Tessa Tattersall & Jason Wong & Mark Hull & Troy Grennan & Adam D., 2025. "Impact of doxycycline pre-exposure prophylaxis (doxyPrEP) for sexually transmitted infections on the microbiome of men who have sex with men on HIV PrEP," Nature Communications, Nature, vol. 16(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61426-5
    DOI: 10.1038/s41467-025-61426-5
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    1. Jacob T. Nearing & Gavin M. Douglas & Molly G. Hayes & Jocelyn MacDonald & Dhwani K. Desai & Nicole Allward & Casey M. A. Jones & Robyn J. Wright & Akhilesh S. Dhanani & André M. Comeau & Morgan G. I., 2022. "Author Correction: Microbiome differential abundance methods produce different results across 38 datasets," Nature Communications, Nature, vol. 13(1), pages 1-1, December.
    2. Jacob T. Nearing & Gavin M. Douglas & Molly G. Hayes & Jocelyn MacDonald & Dhwani K. Desai & Nicole Allward & Casey M. A. Jones & Robyn J. Wright & Akhilesh S. Dhanani & André M. Comeau & Morgan G. I., 2022. "Microbiome differential abundance methods produce different results across 38 datasets," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. I. Vujkovic-Cvijin & O. Sortino & E. Verheij & J. Sklar & F. W. Wit & N. A. Kootstra & B. Sellers & J. M. Brenchley & J. Ananworanich & M. Schim van der Loeff & Y. Belkaid & P. Reiss & I. Sereti, 2020. "HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
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