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

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 () and Adam D. Burgener ()
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Samantha Knodel: Case Western Reserve University
Leighanne Main: Case Western Reserve University
Marlon DeLeon: University of Manitoba
Alana Lamont: University of Manitoba
Joshua Edward: BC Centre for Disease Control
Amit K. Gupta: BC Centre for Disease Control
Laura Noel-Romas: University of Manitoba
Saira Mohammed: BC Centre for Disease Control
Tessa Tattersall: BC Centre for Disease Control
Jason Wong: BC Centre for Disease Control
Mark Hull: BC Centre for Excellence in HIV/AIDS
Troy Grennan: BC Centre for Excellence in HIV/AIDS
Adam D. Burgener: Case Western Reserve University

Nature Communications, 2025, vol. 16, issue 1, 1-10

Abstract: 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 (

Date: 2025
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DOI: 10.1038/s41467-025-61426-5

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