The human microbiome comprises many microorganisms, spanning bacteria, archaea, protozoa, fungi, and viruses. Together, their collective genetic material forms the “microbiome,” and they inhabit various body regions in staggering numbers (Schirmer et al., 2018). Their colonization within the human body stems from intricate interactions with multiple facets of host physiology and metabolism, reflecting a finely tuned relationship. They aid in nutrient absorption and the development of the host’s immune system, playing a vital role in safeguarding the host against infections. In essence, human rely on microbes to maintain their health, while microbes, in turn, depend on the distinctive environment provided by the human body to thrive and coexist in a mutually beneficial relationship.

Based on findings from numerous recent studies utilizing microbiome and omics approaches, alongside data from diverse cohorts of women, it’s evident that the female genital tract harbors a distinct microbial community. Notably, the vaginal microbiome is typically dominated by Lactobacilli (Ravel et al., 2011), maintaining a low-pH environment that protects against pathogens (Miller et al., 2016). Disruption of this community-marked by reduced Lactobacilli abundance and increased microbial diversity-has been associated with inflammation and a heightened risk of persistent HPV infection, ultimately contributing to the development of cervical lesions. However, several knowledge gaps persist. The vaginal microbiota, a key component of the reproductive tract microbiota, is influenced by changes in the gut microbiota (Xu, Mageswaran, et al., 2025). Moreover, the causal relationships among dysbiosis, HPV persistence, and cervical carcinogenesis remain incompletely understood.

This review aims to clarify these concepts and highlight how microbial ecology contributes to HPV susceptibility and disease progression. By distinguishing key microbial niches and emphasizing unresolved mechanisms, the review provides conceptual clarification and points toward areas for future study.

In the typical intestinal microenvironment, an increase in microbiome diversity is a sign of health, while the opposite trend is observed in the female vagina. The vaginal microbiota is a central component of vaginal microbiological ecology. Vaginal dysbiosis is distinguished as a decrease in the number of Lactobacilli and an increase in anaerobic bacteria, resulting in later metabolic and immunological alterations (Mckenzie et al., 2021). Typically, the components of vaginal microecology uphold a dynamic equilibrium. However, when the dominance of Lactobacilli is disturbed and microbial variety escalates, it initiates a sequence of metabolic alterations. Normal vaginal flora and dysbiosis are shown in Figure 2. The resulting increase in vaginal pH disrupts the suppressive role of the vaginal microbiota against additional pathogenic bacteria. Establishment by pathogenic bacteria triggers the secretion of various abnormal metabolites, such as sialidase, β-glucuronidase, coagulase, and neuraminidase, which diminish the thickness of the cervicovaginal fluid (CVF) and impair its protective role. In addition, mucosal immune and inflammatory responses are altered.

BV is a condition caused by multiple types of microorganisms and an exact microbiological definition remains elusive. It is featured by a decrease in Lactobacilli and an elevation in other bacteria typically associated with BV (Pramanick et al., 2019). Nevertheless, these causative organisms are capable of residing in the vaginal flora of healthy women. Meanwhile, individuals with BV typically do not show a notable inflammation. The vaginal mucosa is usually not inflamed or sensitive. Complaints of discomfort or pain are not often heard from female counterparts. Hence, BV is generally categorized as BV rather than vaginitis, and it’s regarded as a significant bacterial imbalance disorder. As depicted in Figure 2, in a healthy vagina during the probiotic phase, the lactic acid colony produces lactic acid. This lactic acid production helps maintain a vaginal pH below 4.5, establishing an acidic condition where acid-resistant bacteria can thrive while inhibiting the growth of pathogenic bacteria. Furthermore, lactic acid exhibits anti-inflammatory properties and serves to protect the epithelial cells. Additionally, it helps maintain the viscoelasticity of the mucus. In contrast, during dysbiosis and BV, there is a restriction in the population of Lactobacilli, leading to a reduction in lactic acid levels. This creates an environment where other pathogenic bacteria, such as Prevotella, Gardnerella, Atopobium, and Mobiluncus, can proliferate. These pathogens produce significant amounts of short-chain fatty acids (SCFAs) from glucose, maltose, and certain amino acids. SCFAs induces the activation of nodular lupus-like receptor protein 3 (NLRP3) inflammatory vesicles and IL-18 secretion in epithelial cells, promoting neutrophil recruitment to inflammatory sites. It also enhances the differentiation and suppressive function of FOXP3 + regulatory T (Treg) cells to mediate inflammation (Yu et al., 2025). In such instances, the integrity of the epithelium is compromised due to bacterial virulence factors, leading to impaired viscoelasticity of the mucus. This creates a pro-inflammatory environment characterized by a foul odor.

During acute HPV infection, the initial immune response is driven by cells with antiviral and bactericidal properties, including mucosal NK cells, macrophages (M1 type during the acute phase and M2 type during the repair phase), and epithelial cells. Inflammatory patterns are infrequently observed due to the evolutionary development of molecular strategies by HPV, enabling them to evade both innate and adaptive immune responses. The HPV16 E7 oncoprotein suppresses TLR9 expression through the NF-κB signaling pathway, inducing an immunosuppressive state that impedes interferon production. This mechanism obstructs immune surveillance via cytokine responses, thereby enabling HPV to achieve immune escape (Mohammed et al., 2025). Infections typically exhibit a notable presence of CD4+/CD25 + regulatory T cells, activated T helper 2 (Th2) cells, and suppression of cytotoxic function, resulting in T cell anergy (Koskela et al., 2000).

The interplay between the vaginal microbiota and the host endocrine system is complex and bidirectional. The vaginal microbiota can metabolize and modulate the local availability of hormones. For instance, certain bacteria express enzymes like β-glucuronidase, which can deconjugate estrogen metabolites, potentially influencing the local hormonal milieu. Conversely, host sex hormones are pivotal regulators of the vaginal ecosystem. Estrogen, in particular, promotes the proliferation of vaginal epithelial cells and glycogen deposition. Animal studies provide insights into the potential depth of microbiota-endocrine interactions. Studies have shown that transferring microbiota from adult male mice to immature females results in shifts in hormone levels (notably elevated testosterone), as well as changes in the metabolome and autoantibody production. For example, one study found no significant differences in bacterial DNA sequencing results obtained from the caecal contents of 4-week-old and 10-13-week-old mice. However, they observed α-diversity discrepancies between the sexes in prepubertal mice. Sequencing of the 16S rRNA gene in the male microbiome, female, and neutered male mice revealed some “unusual” characteristics: the microbiota of female mice was very similar to that of castrated males, with comparable composition and androgen levels (Yurkovetskiy et al., 2013). Similarly, samples collected during pregnancy demonstrated that the composition of the vaginal microbiota tended to shift, mirroring changes in hormone levels and microbial communities. From pregnancy I to pregnancy III, an increase in the solidified bacterial phylum was observed, which is characteristic of the vaginal microbiome of normal women (Amin et al., 2023). On the other hand, during BV, vaginal microbiota dysbiosis has been defined by a variety of bacterial taxa from specific phyla, including Fusarium, Actinobacteria, Pseudomonas, and Bacillus-like phyla (Chaban et al., 2014). Likewise, the vaginal microbiota in premenopausal and perimenopausal women is primarily dominated by the fungal phylum, whereas in postmenopausal women, it is chiefly comprised of Pseudomonas, Bacteroidetes, and Actinobacteria phyla (Amin et al., 2023; Chaban et al., 2014).

It is well-known that there is an interaction between the immune system and the microbiome, involving hormone receptors, various immune mediators, stem cells, different subpopulations of leukocytes, plasma cells, and antibodies such as IgG, IgM, and IgA, along with interleukins and inflammatory proteins. Lactobacilli can directly influence the production of interleukins (IL-1β, IL-6, IL-8, IL-2, IL-10, and IL-17) and play a role in balancing inflammation and anti-inflammation. In terms of immunology, hormones play a pivotal role by actively controlling the synthesis of antimicrobial peptides (such as β-defensins) and cytokines that promote inflammation. These molecules are locally produced by epithelial cells, particularly to protect spermatozoa and prevent infections. Estrogen significantly influences the composition of microbial populations at different life stages. For example, before puberty, the vaginal microbiota is predominantly composed of anaerobic species from the Enterobacteriaceae and Staphylococcaceae families. During puberty, estrogen promotes the accumulation of glycogen in mature epithelial cells (Yurkovetskiy et al., 2013). The digestion of glycogen produces maltotriose and α-dextrin, which serve as essential nutrients for Lactobacilli and facilitate the production of lactic acid (Yurkovetskiy et al., 2013).

As shown in Figure 4, these multifactorial influences highlight the complex interplay between host, viral, microbial, and environmental determinants in shaping cervical disease risk. The microbiota, immune, and endocrine systems form a uniquely specialized unit that ensures vital bodily functions and coordinates essential processes. The microbiota and the immune system collaborate to defend the body against harmful pathogens. Meanwhile, the microbiota and endocrine system ensure normal metabolic activities in organs by managing systemic balance.

Advances in sequencing and multi-omics technologies have enabled the identification of microbiome-based biomarkers to assist with the diagnosis and risk stratification of HPV persistence and cervical lesion progression, as well as predicting them. Technologies such as 16S rRNA sequencing, metagenomics, metatranscriptomics and metabolomics now enable high-resolution profiling of cervicovaginal communities and their functional outputs. This transformation turns the microbiome from a descriptive ecological feature into a clinically relevant diagnostic tool.

Microbial metabolites in the female reproductive system are the end products of metabolic reactions triggered by the interaction between nutrients and microbiota. These metabolites can alter the status of the host through multiple pathways by coordinating physiological functions and response mechanisms. They also serve as key regulatory factors in inflammation of the female reproductive tract, malignant tumors, and pregnancy (Ghartey et al., 2015; Mcmillan et al., 2015). Typical vaginal microbial metabolites, such as lactic acid, hydrogen peroxide, ethanol and SCFAs, are emerging as functional biomarkers that reflect the health of the cervix and vagina (Liu et al., 2022). Increased SCFAs in the female reproductive system lead to a mixed anaerobic flora and induce inflammation (Aldunate et al., 2015; Amabebe and Anumba, 2020). These mixed anaerobic flora include Streptococcus, Bacteroides, Gardnerella, Prevotella, Mycoplasma, and Mobiluncus, which are commonly found in female genital tract diseases such as BV and vulvovaginal candidiasis (VVC) (Aldunate et al., 2015, Ceccarani et al., 2019, Vitali et al., 2015). Anaerobes associated with BV can produce SCFAs in the female reproductive system through carbohydrate fermentation and amino acid catabolism. The most common SCFAs found in the female reproductive tract include propionate, acetate, isovalerate, isobutyrate, and n-butyrate (Dandona et al., 2004). In vaginal dysbiosis, acetate and propionate often reach elevated millimolar concentrations (10–50 mM), markedly higher than levels observed in Lactobacillus-dominant states. In addition, SCFAs signal through G-protein coupled receptors such as GPR41 and GPR43, which are expressed on cervical epithelial and immune cells (Ceccarani et al., 2019). Activation of these receptors modulates cytokine secretion, epithelial permeability, and neutrophil recruitment, suggesting a direct pathway by which dysbiotic metabolic profiles influence local immunity. High concentrations of acetate and butyrate have been shown to alter tight-junction proteins and histone acetylation patterns in cervical epithelial cells, potentially facilitating viral entry and supporting HPV persistence. Taken together, the composition of the microbiome and its metabolic outputs provide a rich source of biomarkers for the early diagnosis, prognosis and prediction of risk. Based on this concept, several microbial taxa and multi-omics signatures have been suggested as potential clinical biomarkers.

Changes in the vaginal microbiome can be used to screen for precancerous lesions of cervical cancer. Certain bacteria can serve as biomarkers to help us determine whether HPV infection can develop into cervical cancer. Traditional biomarkers include immune markers and HPV genotyping. Hr-HPV can integrate into the host genome and, through its multi-copy presence in cells, be released in the form of circulating tumor DNA (ctDNA). Therefore, ctHPV DNA is a potential biomarker for cervical cancer (Sivars et al., 2023). Type-specific total viral load may serve as a robust diagnostic indicator for High-grade squamous intraepithelial lesion (HSIL) in HPV types 16, 18, and 58 (Kim et al., 2020). However, these markers alone are insufficient for accurate risk stratification. Recently, increasing attention has been directed toward microbial biomarkers, particularly those from the gastrointestinal and vaginal microbiota, due to their close association with the pathogenesis of HPV infection and cervical lesions. Numerous studies have shown that alterations in vaginal microbiome diversity may serve as early indicators for the diagnosis and prevention of various HPV-related conditions. It has been reported that Gardnerella vaginalis can disrupt cervical-vaginal microbial homeostasis and may serve as a key biomarker for the progression of HPV infection to HSIL (Kudela et al., 2021). Likewise, other studies have indicated that Streptococcus sanguinis, anaerobic cocci, and anaerobic digestible streptococci may also function as potential biomarkers for HSIL (Mitra et al., 2015). Continued advancements in this field have the potential to improve current diagnostic frameworks.

In recent years, the vast amount of information and data about the microbiome has revolutionized the field of microbiology. Multi-omics approaches provide a more comprehensive understanding of the vaginal microbiome and its interactions with HPV. Metagenomics identifies the composition of microbes and their functional genes. Metatranscriptomics captures the expression of genes in microbes and hosts (Jiang et al., 2019). Metabolomics quantifies bioactive metabolites, such as SCFAs and lactate, that influence mucosal immunity. Each “omics” layer provides different, yet complementary, information. Combining them provides a more complete view of HPV-microbiome interactions. Recent studies illustrate the value of this approach. Multi-omics profiling has revealed that HPV-positive women exhibit increased microbial diversity and an enrichment of Gardnerella-related metabolic pathways. There are also shifts toward pro-inflammatory metabolites, such as acetate and propionate. Furthermore, metatranscriptomic analyzes have demonstrated that HPV infection alters the expression of host epithelial immune genes, including those in interferon-related pathways. Meanwhile, metabolomic signatures have been shown to distinguish cervical intraepithelial neoplasi (CIN)1 from high-grade CIN lesions with high accuracy. Together, these findings emphasize that multi-omics integration can reveal biomarkers of HPV persistence and identify molecular pathways linking dysbiosis to cervical carcinogenesis.

The World Health Organization (WHO) characterizes probiotics as live microorganisms that, when consumed in appropriate quantities, offer advantageous effects on the host’s health. Metronidazole and lincomycin are commonly used antibiotics to treat BV. The efficacy of antibiotics in treating bacterial vaginosis or antifungals in addressing VVC is not always optimal, and recurrence rates tend to be high. While antibiotics may effectively inhibit anaerobic overgrowth, they often fail to restore Lactobacilli to their optimal levels. Extended use of antibiotics is also linked to numerous adverse effects and an increased risk of bacterial resistance. Hence, with the growing recognition of the role of Lactobacilli in maintaining vaginal health, vaginal probiotics containing Lactobacillus strains have become increasingly popular as both preventive and therapeutic interventions for vaginal dysbiosis. Vaginal probiotics containing Lactobacilli have been extensively researched and developed for the treatment of BV and VVC. Pregnant women with VVC have shown promising efficacy and safety after using probiotics, significantly improving their quality of life. Furthermore, probiotics show promise in offering some potential benefits to individuals experiencing constipation (Ang et al., 2022a; Ang et al., 2022b). For pregnant patients experiencing recurrent staphylococcal infections, probiotic preparations are a promising therapeutic option if antifungal drugs are contraindicated. Besides their therapeutic benefits, long-term oral probiotics offer protection for healthy women as well (Reid et al., 2003). Most probiotics play a key role in restoring the composition of the vaginal microbiota (Van De Wijgert and Verwijs, 2020; Lagenaur et al., 2021).

By replenishing diminished Lactobacilli, probiotics can offer protective functions comparable to natural Lactobacilli. These functions encompass establishing a robust physical barrier, stimulating the immune system, and decreasing the expression of E6 and E7 proteins. Studies have demonstrated that the Lactobacillus strain LH23 can reduce the expression of E6 and E7 proteins, thereby inhibiting cervical cancer cell proliferation and inducing apoptosis (Hu et al., 2023). Additionally, recent findings indicate that taurine produced by Lactobacillus rhamnosus markedly decreases endometrial cancer cell viability, highlighting its targeted anticancer effects (Lawore et al., 2024). Our research findings indicate that women are more likely to develop vaginal dysbiosis in cases of persistent HPV infection. In this context, using probiotics might promote HPV clearance and is associated with a reduced incidence of uterine lesions in some studies (Medina-Rivero et al., 2025). Women experiencing persistent vaginal dysbiosis should consider using probiotics, reduce sexual frequency, and employ protective measures such as condom use to further mitigate the risk of complications (Figure 5).

Another method to restore vaginal microbiota is by using probiotics. Prebiotics are organic compounds that remain undigested or unabsorbed by the host, yet they selectively foster the metabolism and growth of beneficial bacteria within the body, consequently enhancing host health. Probiotics can enhance HPV clearance through immune regulation, competitive elimination of pathogens, and production of protective metabolites (Porcaro et al., 2025). We summarized some studies on the treatment of HPV infection and the prevention of cervical cancer with probiotics using Table 1. In cases of intestinal diseases, oral intake of prebiotics can improve intestinal conditions and promote the activity of Lactobacilli. Likewise, in the vaginal environment rich in Lactobacilli, prebiotics can exert comparable function. A large number of researchers have found that the disaccharide lactofructose broadly and specifically stimulates the growth of vaginal Lactobacilli, including Bacteroides fragilis, without promoting the growth of bacteria associated with bacterial vaginosis (Collins et al., 2018). Studies have additionally shown that probiotic maltose gel facilitates the transition of vaginal microbiota in rhesus monkeys from domination by BV-associated bacteria to a prevalence of Lactobacilli (Zhang et al., 2020). According to clinical studies, the combination of Lactobacillus rhamnosus BMX54 with lactose can restore the vaginal microbiota and regulate vaginal pathological pathways (Baldacci et al., 2020). However, due to the lack of relevant clinical and preclinical studies, whether this combination can benefit patients with HPV infection needs to be further explored in the future. Despite these positive signals, the clinical evidence remains limited by several key factors: small sample sizes, heterogeneity in probiotic strains, dosages, and administration routes, short follow-up periods, and a primary focus on BV and VVC rather than HPV clearance as the primary endpoint. Consequently, while certain probiotic regimens show promise, they cannot yet be recommended as a standard clinical intervention for preventing or treating HPV-related cervical disease.

Numerous studies have shown that changes in microbial diversity and disturbances in microbiome composition can be linked to the onset of various diseases. Our assessment indicates that a reduction in Lactobacilli within the vaginal microbiota is linked to sustained HPV infection and the advancement of cervical lesions. The use of probiotics and prebiotics can aid in reestablishing the normal vaginal microbiota, thereby potentially impeding the progression of cervical lesions (Figure 6).

Despite extensive research on the relationship between the vaginal microbiome and HPV infection, most of the available data are derived from cross-sectional designs, which limit the scope for interpretation to correlations rather than causations. Additionally, inconsistent findings across studies are due to heterogeneity in sequencing platforms, CST classification methods and analytical pipelines. The dynamic and unstable nature of CSTs, coupled with hormonal fluctuations, sexual behavior and behavioral confounders, makes interpreting microbiome-HPV interactions even more challenging. These variables complicate the exclusion of external influences and often result in inconsistent or non-reproducible findings. However, it should be noted that it is unclear whether dysbiosis leads to persistent HPV infection or is a consequence of viral suppression of mucosal immunity. There is also insufficient mechanistic insight into how microbial metabolites (such as SCFAs) alter epithelial junctions and modulate inflammation. The intricate interplay between the microbiome, immune responses and HPV oncogene expression requires further investigation.

To address these challenges, future research should prioritize longitudinal cohort designs to clarify the temporal sequence between microbiome alterations and HPV infection. Integrating multi-omics platforms, which encompass metagenomics, metatranscriptomics, metabolomics and immunoassays, could help to identify the microbial metabolites and host pathways that drive HPV persistence or tumor formation. In future clinical trials, standardized microbiome-related markers such as SCFAs, lactate enantiomers and mucosal immune biomarkers could be used as secondary endpoints alongside HPV clearance rates. Well-designed, controlled clinical trials are needed to determine the therapeutic potential of probiotics, prebiotics, vaginal microbiota transplantation and metabolite-targeted therapies. Addressing these challenges will help future research clarify the clinical utility of microbiome modulation in preventing HPV persistence and cervical disease progression.