The female microbiome in HIV prevention, pathogenesis, and treatment

Abstract

Purpose of review:

To summarize the relationship of vaginal and gut microbiomes with HIV transmission, pathogenesis, and treatment, focusing on women’s health.

Recent findings:

Bacterial vaginosis (i.e., vaginal microbiome dysbiosis) is a well-established risk factor for HIV acquisition, and recent research focused on molecular mechanisms and biomarkers for HIV acquisition related to vaginal microbiota. Recent clinical trials reported on probiotics to treat bacterial vaginosis with the goal of HIV prevention; however, durability of treatment response remains sub-optimal. The vaginal microbiome may impact efficacy of pre-exposure prophylaxis (PrEP) and antiretroviral therapy (ART) in vaginal tissue, with recent literature examining vaginal microbiota and long-acting PrEP vaginal rings. Some research also suggests effects of PrEP or ART initiation on the vaginal microbiome. Regarding the gut microbiome, associations with HIV status may differ more by sexual practices than biological sex, and sex-specific roles of gut microbiota in HIV pathogenesis and treatment are unknown. Interactions of the gut microbiome with estrogens could underlie a role of gut microbiota in health of women with HIV.

Summary:

The vaginal microbiome remains an important factor in HIV acquisition, prevention, and treatment in women. The gut microbiome has roles in HIV pathogenesis and treatment, but women-specific effects are unclear.

INTRODUCTION

Sex differences in HIV infection, including HIV acquisition, pathogenesis, and treatment response, can be attributed to a variety of factors spanning anatomy, genetics, immunity, and hormones [1]. For example, vaginal inflammation increases risk of HIV acquisition [2, 3], which may contribute to higher rates of HIV infection from heterosexual intercourse in women vs. men [4]; while the role of estrogen in HIV latency may lead to sex differences in HIV pathogenesis and cure strategies [5]. The human microbiome may also play important roles in sex differences in HIV. Spanning many anatomical sites, human-resident microbial communities differ by sex [6, 7], and contribute to host metabolism, immunity, and inflammation, underlying their role in disease susceptibility and sex differences therein. In this review, with focus on women’s health, we summarize the relationship of vaginal and gut microbiomes with HIV transmission, pathogenesis, and treatment, paying particular attention to recent insights from female populations.

VAGINAL MICROBIOME IN HIV ACQUISITION

A healthy vaginal microbiome in reproductive age women is characterized by low diversity and dominance of Lactobacillus, which maintain an acidic environment aiding in protection from pathogens [8]. In contrast, a diverse vaginal microbiome depleted in Lactobacillus and enriched in other anaerobes (e.g., Gardnerella, Prevotella), a condition termed bacterial vaginosis (BV), is associated with increased vaginal pH, inflammation, and risk of sexually transmitted infections (STIs) [9]. BV, affecting 25% of women globally with greatest burden in resource-limited settings [9], has been consistently associated with increased risk of HIV acquisition [10]. Over the last decade, research has strongly supported the notion that microbiome dysbiosis in the female reproductive tract promotes local inflammation [11, 12], which increases risk of acquiring HIV [2, 3, 13–19].

To address the vaginal microbiome as an important risk factor for HIV acquisition, recent studies focused on further clarifying underlying mechanisms. Smoorenburg et al. (2025) reported that Prevotella timonensis, a BV-associated bacterium, increased HIV uptake in dendritic cells present in vaginal tissue, and enhanced HIV transmission to target cells [20]. This new data, taken together with other recent data showing P. timonensis induces HIV uptake and transmission in vaginal Langerhans cells [21], and increases HIV uptake and production in vaginal CD4+ T cells [22], suggests that P. timonensis may underlie BV-related HIV susceptibility, though further research is needed to isolate molecular mechanisms by which P. timonensis enhances viral uptake and transmission [20–22].

Recent observational studies provided new insights into vaginal microbiome biomarkers of HIV risk. In a nested case-control study among 586 African women, Srinivasan et al. (2024) found that 14 bacterial taxa in vaginal swabs were associated with greater HIV acquisition risk, while Lactobacillus crispatus was associated with reduced risk [23]. The 14 risk-associated taxa (not typical BV-associated bacteria) were correlated with higher vaginal proinflammatory cytokines IL-1α and IL-1β, and served together with immune biomarkers to classify risk of HIV [23]. Meanwhile, a point-of-care cytokine biomarker lateral flow test for STI and BV screening, the Genital InFlammation Test (GIFT) [24], has been developed based on research showing vaginal cytokines IL-1α, IL-1β, and IP-10 performed well in classification of asymptomatic STIs and vaginal microbiome dysbiosis [25]. Ramboarina et al. (2024) reported that the GIFT device is being prospectively evaluated to determine its performance, acceptability, and cost-effectiveness as a routine care strategy to identify women at high risk of HIV in resource limited countries [24].

MODIFICATION OF VAGINAL MICROBIOME FOR HIV PREVENTION

Given the well-known association of BV with HIV incidence, modification of the vaginal microbiome for HIV prevention in women is of utmost importance; however there are limited effective treatments for BV [14]. Standard-of-care antibiotic treatment (i.e., metronidazole) for BV often fails or is followed by recurrence [26, 27], with no improvement by addition of vaginal probiotics based on current strategies [28]. Standard BV treatment may lead to complex outcomes regarding HIV susceptibility, with one study showing reduced HIV entry into cervical CD4+ T cells but increased chemokine levels associated with HIV acquisition, the latter related to Lactobacillus iners colonization [29]. Further, metronidazole was shown to reduce genital inflammation through reductions in BV-associated bacteria rather than increases in Lactobacillus [30], and may increase vaginal fungi with unclear implications [31]. Given limitations and complexities with standard BV treatment, novel treatments are needed to move the HIV prevention field forward.

Recent clinical trials tested new treatments for improving the vaginal microbiome in women with high HIV risk. Gill et al. (2025) reported on a phase 1 clinical trial of intravaginal estradiol and/or vaginal or oral Lactobacillus probiotics for 30 days, among 50 African, Caribbean and Black women in Canada [32], the rationale based on estrogen supporting glycogen production in the vaginal mucosa, which should promote Lactobacillus and is typically prescribed for genitourinary symptoms in menopausal women [8, 33]. While the trial demonstrated success in safety and tolerability, future publications will investigate secondary outcomes including vaginal Lactobacillus, inflammation, and HIV target cells [32]. Hemmerling et al. (2025) conducted a phase 2 randomized, placebo-controlled trial of a vaginal live therapeutic, LACTIN-V (Lactobacillus crispatus CTV-05) among women at high HIV risk in South Africa [34]. Forty-five women with BV completed metronidazole treatment and were randomized 2:1 to LACTIN-V or placebo for 4 weeks. LACTIN-V increased vaginal L. crispatus after 4 weeks, though the effect was minimized at 8 weeks [34]. These results were consistent with a prior larger trial of LACTIN-V in the U.S. with similar design for 11 weeks, in which LACTIN-V significantly increased L. crispatus and lowered incidence of BV recurrence at 12 weeks [35]. Additionally in the South African trial, endocervical CD4+ HIV target cells increased in the placebo but not LACTIN-V group at 4 weeks, suggesting that treatment with LACTIN-V after metronidazole has potential to reduce risk of HIV acquisition [34], though further strategies are needed to support durability past the treatment period. Finally, Zulaika et al. (2024) reported a protocol for a single-arm trial of menstrual cups to reduce BV and HIV/STI incidence among women in Kenya [36], which is ongoing.

VAGINAL MICROBIOME IN PRE-EXPOSURE PROPHYLAXIS (PrEP)

Treatment with PrEP has reduced HIV transmission in high-risk populations, however early PrEP trials showed high variability of efficacy in women [37–39]. Almost a decade ago, Klatt et al. demonstrated that the vaginal microbiome modifies efficacy of topically-applied vaginal tenofovir gel in protection against HIV [40], which was a breakthrough in understanding variable efficacy of PrEP in women. Specifically, tenofovir gel significantly reduced incidence of HIV in women with Lactobacillus-dominated vaginal microbiomes, but not in women dominated by Gardnerella or other BV-associated bacteria, since these bacteria can rapidly metabolize and deplete tenofovir in vaginal mucosa [40, 41]. Further, Lactobacillus-dominant women in the trial faced greater HIV risk if using injectable depot medroxyprogesterone acetate [42]. On the other hand, oral PrEP efficacy may not be influenced by the vaginal microbiome [43–45].

With great interest in long-acting PrEP to overcome daily adherence issues, recent research examined tenofovir vaginal rings and whether vaginal microbiota may influence drug release. In a phase 1 randomized trial of a 90-day tenofovir vaginal ring, Thurman et al. (2022) found that women with non-Lactobacillus-dominated vaginal microbiomes had higher release rates of tenofovir from vaginal rings and lower tenofovir concentration in vaginal tissue, which may be due to higher vaginal pH promoted by non-Lactobacillus-dominated microbiota [46]. However, this did not impact in vitro HIV inhibition in vaginal fluid, which was increased in all women [46]. More recently, Liu et al. (2024) reported that vaginal microbiota were unrelated to residual tenofovir in returned rings in a phase 1 randomized trial of a 90-day tenofovir vaginal ring [47]. To target BV and HIV prevention simultaneously, a combination vaginal ring of metronidazole and PrEP is also under development [48].

Initiation of PrEP may also impact the vaginal microbiota. In a study of 255 pregnant women with or without HIV in Malawi, Saidi et al. (2025) observed that oral PrEP initiation in women without HIV increased vaginal microbiome diversity, decreased L. iners, and increased Gardnerella, a shift associated with higher risk of pre-term birth [49]. However, Mazibuko-Motau et al. (2022) did not observe an impact of oral PrEP initiation on longitudinal shifts in vaginal microbiota among South African women [50].

VAGINAL MICROBIOME IN WOMEN WITH HIV

Given the role BV plays in susceptibility to HIV, it is difficult to disentangle whether HIV infection also contributes to BV development [45], though research suggests that HIV is associated with BV persistence (but not incidence), particularly in immunocompromised women with HIV [51]. BV is associated with obstetric complications including pre-term birth and spontaneous abortion [9], and increased vaginal HIV shedding which impacts transmission [17, 52], highlighting importance of BV treatment among women with HIV. Research is mixed on how antiretroviral therapy (ART) and/or hormonal contraception impact the vaginal microbiota and vaginal HIV shedding among women with HIV, with some research suggesting no impact of ART initiation on the vaginal microbiome in women with HIV [53]. However, in the study of pregnant women with or without HIV in Malawi, ART initiation decreased vaginal microbiome diversity and increased abundance of Prevotella, Gardnerella, and Peptostreptococcus among women with HIV [49]. In a clinical trial of an ethinyl estradiol/etonogestrel vaginal ring among 74 women with HIV, Tobin et al. (2024) reported that vaginal ring use increased prevalence of Lactobacillus-dominated vaginal microbiomes, which were associated with lower risk of vaginal HIV shedding [54].

Some research suggests that the vaginal microbiome may also modulate ART efficacy in the female genital tract in women with HIV [55], similar to its modulation of PrEP efficacy in women without HIV, reviewed above. Lantz et al. (2023) found that ART drug concentrations were positively correlated with anaerobic bacteria in cervicovaginal fluid, which differed by ART regimen, among 73 women with HIV in Malawi [56]. Other reports by that group noted positive correlations of Lactobacillus with lamivudine triphosphate concentration in cervicovaginal fluid among 50 women with HIV in Uganda receiving tenofovir/lamivudine-based ART [57, 58].

GUT MICROBIOME IN WOMEN WITH HIV

Gut microbiota carry out many critical functions including metabolism of exogenous and endogenous compounds, and modulation of immunity and inflammation. Therefore, the impact of HIV on the gut microbiome, and role of gut microbiota in HIV pathogenesis and treatment, has been a focus of HIV research over the past two decades. It is generally recognized that HIV infection leads to gut microbiome dysbiosis, in the form of reduced diversity and altered composition, though altered taxa may vary across studies [59–61]; while ART in part may reverse gut microbiome dysbiosis [62]. Microbial translocation due to impaired gut barrier is a suspected cause of immune activation and inflammation in HIV [63]. Gut microbiome alterations in HIV may contribute to non-communicable diseases [64], and gut microbiome-targeted therapies (e.g., fecal microbiome transplant, probiotics) have been investigated to reduce inflammation and morbidity in people with HIV, though progress is ongoing [65, 66].

While these topics have been reviewed extensively [59, 62, 64–66], here we focus on the gut microbiome in women with HIV specifically. There has been limited research on whether the gut microbiome is associated with HIV acquisition risk in women, likely because (1) the vaginal microbiome is more relevant for HIV acquisition in women given risk of vaginal transmission, and (2) the gut or rectal microbiome is more relevant to risk of HIV in men who have sex with men (MSM) given risk of rectal transmission [67–69].

Whether there are sex differences in the association of HIV with the gut microbiome is currently unknown, though there is sexual dimorphism of the gut microbiome [70–72]. MSM sexual practices, which are related to Prevotella-rich gut microbiome composition, have confounded associations of HIV status with the gut microbiome [73] and pose difficulties in disentangling effects of sex, sexual practices, and HIV on gut microbiota. In a meta-analysis, HIV was associated with decreased gut microbiome diversity among women and men who have sex with women, but not MSM [60], supporting heterogeneity by sexual practices, but not biological sex, in the relationship of HIV and the gut microbiome. A number of studies reported comparisons of the gut microbiome in women with vs. without HIV [74–77], but without comparable men to determine sex-specific effects. Our group has uncovered relationships of the gut microbiome with various outcomes in women with and without HIV, including diabetes [78], subclinical atherosclerosis [79, 80], sleep [81], and cognitive function [82], but without comparable men to examine sex specificity. However, in a recent large analysis of aging and the gut microbiome, we found similar associations of age with gut microbiota across sex and HIV strata [83].

Research by our group has also focused on relationships of hormonal factors (menopause, sex hormones) with the gut microbiome in women with and without HIV. The gut microbiome is hypothesized to “recycle” estrogens and other sex hormones via deconjugation reactions which facilitate hormone reabsorption from the gut [6] – this relationship may underlie associations of the gut microbiome with hormonal factors, which may be particularly important in women with HIV who have lower estrogen levels [84, 85], and possible earlier menopause with more severe symptoms [86–91]. In a cross-sectional study of 446 women with and without HIV in the U.S., we observed compositional differences in the gut microbiome for post- vs. pre-menopausal women with HIV, including depletion of Faecalibacterium prausnitzii and abundance of the β-glucuronidase gene, involved in estrogen deconjugation; while these differences were not observed among women without HIV [92]. The menopause-related gut microbiome profile in women with HIV was associated with adverse metabolomic and proteomic profiles and elevated waist-to-hip ratio, suggesting contribution to cardiometabolic risk [92]. Further, in cross-sectional analysis of 197 post-menopausal women with and without HIV, we found positive associations of serum estrogens with gut microbiome diversity, Alistipes and Collinsella species, and the β-glucuronidase gene; while estrone-related gut microbiota were associated with reduced odds of carotid artery plaque [85], though sample size was limited for HIV-stratified analysis. This research highlights that via interactions with sex hormones, the gut microbiome may play a unique role in women’s health, particularly for women with HIV. It is also possible that via estrogen recycling, the gut microbiome could positively influence the vaginal microbiome [8] to reduce BV and HIV risk, though this has never been studied.

CONCLUSIONS

Vaginal microbiome dysbiosis (i.e., BV) has become a well-established risk factor for HIV acquisition. Molecular mechanisms of vaginal microbiota contributing to acquisition are still being uncovered, as are vaginal microbiome-related biomarkers of HIV risk. Current probiotic therapies to resolve BV for HIV prevention show promise but limited durability; more research is needed to identify effective, durable BV treatments. Additionally, the vaginal microbiome may alter PrEP and ART efficacy in vaginal tissue through drug metabolism, particularly for topical PrEP. Evidence for effects of PrEP or ART initiation on vaginal microbiota remains limited. The effect of HIV on the gut microbiome may differ more by sexual practices than biological sex, while interactions of menopause and estrogens with the gut microbiome may have implications for cardiometabolic health in women with HIV. Future research can explore whether gut microbiota have a sex-specific role in health of women with HIV.

KEY POINTS.

• Dysbiosis of the vaginal microbiome, often called bacterial vaginosis, is a well-established risk factor for HIV acquisition.

• More research is needed to identify effective and durable treatments for bacterial vaginosis to promote HIV prevention in women.

• The vaginal microbiome may alter PrEP and ART efficacy through drug metabolism.

• Sex-specific effects of the gut microbiome in HIV pathogenesis and treatment are unclear.