# Gut microbiome composition influences immunologic alterations in the blood and gut of HIV-positive and HIV-negative men who have sex with men

**Authors:** Charles Preston Neff, Janet Siebert, Mallory Karr, Ricky Lippincott, Rachel Kvaal, Amy T. Noe, Elena Wall, Nichole Nusbacher, Suzanne Fiorillo, Blair P. Fennimore, Thomas B. Campbell, Catherine Lozupone, Brent E. Palmer

PMC · DOI: 10.3389/fimmu.2025.1707736 · Frontiers in Immunology · 2026-01-02

## TL;DR

The gut microbiome affects immune responses in HIV-positive and HIV-negative men who have sex with men, with distinct immune changes linked to HIV status and sexual behaviors.

## Contribution

The study reveals how gut microbiome-immune interactions differ in HIV+ and HIV- men who have sex with men, influenced by both infection and sexual risk behaviors.

## Key findings

- HIV+ individuals showed reduced CD4⁺ CD103⁺ and CD8⁺CD103⁺ T cells in colonic biopsies.
- High-risk sexual behaviors in MSM correlated with reduced MAIT cells in the blood.
- Network analysis identified tissue-specific immune-microbiome relationships shaped by HIV and MSM factors.

## Abstract

HIV infection and factors associated with sexual activity among men who have sex with men (MSM) can dysregulate relationships between the gut microbiome and immune system.

To explore these relationships in depth, blood and colonic biopsy samples from HIV+ and HIV- MSM and non-MSM were analyzed using Cytometry by Time of Flight (CyTOF). Immune profiles were then integrated with gut microbiome composition and MSM-related behaviors.

HIV infection status influenced immune cell composition in colonic biopsies, marked by a loss of CD4⁺ CD103⁺ and CD8⁺CD103⁺ tissue-resident T cells and group 3 innate lymphoid cells (ILC3s). In the blood, HIV status was linked to reductions in circulating group 2 innate lymphoid cells (ILC2s), and naïve CD8⁺ T cells, while mucosal-associated invariant T (MAIT) cells were reduced in MSM engaging in high-risk sexual behaviors regardless of HIV status. Network analysis revealed distinct, tissue-specific relationships between immune cell populations and gut microbial taxa, further shaped by both HIV infection and MSM-associated factors.

These findings provide new insights into host:microbe interactions, with implications for immune regulation, HIV persistence, and transmission among MSM.

## Full-text entities

- **Genes:** CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, ITGAE (integrin subunit alpha E) [NCBI Gene 3682] {aka CD103, HUMINAE}
- **Diseases:** HIV (MESH:D015658)
- **Species:** gut metagenome (species) [taxon 749906], Homo sapiens (human, species) [taxon 9606], Human immunodeficiency virus 1 (no rank) [taxon 11676]

## Full text

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## Figures

5 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12808405/full.md

## References

102 references — full list in the complete paper: https://tomesphere.com/paper/PMC12808405/full.md

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Source: https://tomesphere.com/paper/PMC12808405