Pre-treatment Microbiome Diversity and Function is associated with Expansion of Cytotoxic and Regulatory Immune Populations after N-803 treatment in People with HIV

Chakrawarti, A.; Cromarty, R. T.; Basting, C. M.; Anderson, J.; Schroeder, T.; Escandon, K.; Shields-Cutler, R.; Swanson, E.; Soon-Shiong, P.; Safrit, J. T.; Sender, L. S.; Reddy, S.; Miller, J.; Rhein, J.; Schacker, T.; Klatt, N. R.

doi:10.1101/2025.10.01.679827

bioRxiv · 10.1101/2025.10.01.679827

Pre-treatment Microbiome Diversity and Function is associated with Expansion of Cytotoxic and Regulatory Immune Populations after N-803 treatment in People with HIV

Chakrawarti, A.·Cromarty, R. T.·Basting, C. M.·Anderson, J.·Schroeder, T.·Escandon, K.·Shields-Cutler, R.·Swanson, E.·Soon-Shiong, P.·Safrit, J. T.·Sender, L. S.·Reddy, S.·Miller, J.·Rhein, J.·Schacker, T.·Klatt, N. R.

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Abstract

BackgroundN-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood. MethodsIn this longitudinal metagenomic study, we analyzed fecal microbiomes from ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment. ResultsOverall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii increased significantly after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8+ and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA+ cells. MaAsLin2 analyses further associated short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers. ConclusionsThese results indicate that gut microbiome diversity prior to immunotherapy influences host response and suggest that microbiome-based strategies could improve efforts to cure HIV.

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Chakrawarti, A., Cromarty, R. T., Basting, C. M., Anderson, J., Schroeder, T., Escandon, K., Shields-Cutler, R., Swanson, E., Soon-Shiong, P., Safrit, J. T., Sender, L. S., Reddy, S., Miller, J., Rhein, J., Schacker, T., Klatt, N. R.. 2025-10-01. Pre-treatment Microbiome Diversity and Function is associated with Expansion of Cytotoxic and Regulatory Immune Populations after N-803 treatment in People with HIV. https://doi.org/10.1101/2025.10.01.679827

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