Vaginal microbiota is a complex ecosystem of bacteria inhabiting the vagina which plays a crucial role in women’s health, including during pregnancy. As an example, a higher concentration of lactobacilli appears to reduce the risk of miscarriage.

Among the various lactobacilli in the vaginal flora, Lactobacillus iners is particularly interesting as this bacterium is found in both healthy and pathological microbiota, raising questions about its exact role. A study conducted on 91 Chinese women in the third trimester of pregnancy provides new insights.

Higher levels of L. iners in healthy women

The study shows that one in two healthy women harbors a vaginal flora dominated by L. iners, whereas fewer than one in three women in the “unhealthy” group (gestational diabetes (sidenote: Gestational diabetes Gestational diabetes can develop during pregnancy in women who don't already have diabetes, usually around the 24th week. Testing is typically done between 24 and 28 weeks. It occurs when the body can't produce enough insulin during pregnancy—a hormone that allows blood sugar (glucose) to enter the cells to be used for energy. As a result, blood sugar levels (glycemia) become higher than normal. Every year, 5% to 9% of pregnancies in the U.S. are affected by gestational diabetes. Proper management of gestational diabetes helps ensure a healthy pregnancy and a healthy baby. CDC ) , pregnancy complications, etc.) have this type of microbiota. Conversely, a flora dominated by L. crispatus is more frequent among expectant mothers with health issues.

For example, this type of microbiota is present in 57% of women with gestational diabetes.

Could the higher frequency and abundance of L. iners explain the good health of pregnant women? Researchers believe this could be true. This is because a higher presence of L. iners means an enhanced production of beneficial microbial molecules by this bacterium. This includes an increased biosynthesis of a compound with the intimidating name “tetrahydrofolate” which helps maintain moderate inflammation in late pregnancy.

Different strains of L. iners

However, not all L. iners strains are the same. Among the seven strains identified in pregnant women, three strains associated with bacterial vaginosis (sidenote: Bacterial vaginosis Bacterial vaginosis (BV) is a type of vaginal inflammation caused by an imbalance of the bacterial species that are normally present in the vagina. ) were particularly adept at forming feared biofilms, which serve as shelters where pathogens can multiply. Four other strains (some associated with vaginosis, others not) appeared capable of inhibiting the growth of the pathogen Gardnerella vaginalis. In short, each L. iners strain has its own characteristics—and likely several tricks up its “bacterial” sleeve. But some strains could help maintain the stability of the vaginal ecosystem in pregnant women.

Diversity in vaginal microbiota profiles

Vaginal microbiota is made up of five different community state types (CSTs), including three protective CSTs (respectively dominated by Lactobacillus crispatus, Lactobacillus gasseri or Lactobacillus jensenii), one disruptive CST, and one—CST III—dominated by L. iners, whose role in vaginal health remains debated. This is because the bacterium may be protective or disruptive—while it seems to be an integral part of a healthy vaginal microbiome, it is paradoxically also abundant in pathological and dysbiotic conditions and has even been implicated in colonization by Group B Streptococcus during pregnancy.

More L. iners in healthy expectant mothers

To better understand the relationship between microbial flora and vaginal health, Chinese researchers focused on the particular case of pregnant women in their third trimester—either healthy (34 women) or not (61 women with gestational diabetes, complications, infection, etc.). Their results highlight the persistence of lactobacilli predominance and the maintenance of alpha diversity across all expectant mothers.

Most notably, the type dominated by L. iners was less common in the group of sick women (31.15%) than in the group of healthy women (50%). In addition, L. iners was relatively more abundant (as a percentage of the species present) in healthy women.

Altered metabolic pathways

The increased abundance of L. iners in healthy pregnant women was associated with the overexpression of metabolic pathways favorable to a healthy pregnancy—for example, tetrahydrofolate (sidenote: Tetrahydrofolate a coenzyme derived from folic acid, primarily involved in the synthesis of nucleic acid bases (purines and pyrimidines), which constitute the DNA and RNA of genetic material. Tetrahydrofolate (THF) is also involved in the synthesis of amino acids, including methionine, histidine, and serine. ) biosynthesis, which may play various roles (microbial folate synthesis, a slightly pro-inflammatory state).

But the higher abundance of this bacterium in healthy women was also associated with glycosyltransferase (sidenote: Glycosyltransferase a membrane-associated enzyme that catalyzes the transfer of a sugar moiety onto a protein, resulting in the formation of a glycoprotein. In pathogenic bacteria, these glycoproteins have been implicated at various stages of the infection process.

Explore: Tomás JM, Fulton KM, Twine SM et al. Generation of Null Mutants to Elucidate the Role of Bacterial Glycosyltransferases in Bacterial Motility. J Vis Exp. 2022 Mar 11;(181). ) synthesis routes and antibiotic resistance, compared with women suffering from pathologies. These mechanisms may reflect the dynamic adaptation of the microbiota to the immune and hormonal environment characteristic of the third trimester of pregnancy.
 

Seven very different strains of L. iners

More in-depth analyses show that not all L. iners are alike. Among the seven strains of L. iners identified by the authors, three strains associated with bacterial vaginosis (versus four strains associated with good health) proved to be more efficient at forming biofilms, thanks to genes coding for the proteins involved. The team also showed that five of the seven identified strains (whether associated with bacterial vaginosis or not) inhibited the growth of the pathogen G. vaginalis, which is implicated in preterm birth.

These results suggest that L. iners may exert a protective influence depending on environmental conditions and the strains involved. A microbiota dominated by certain strains of L. iners could therefore contribute to the prevention of complications linked to persistent dysbiosis.

Explore the latest insights on the conditions that promote a balanced vaginal microbiota: 

Colorectal cancer (CRC) is the third most common type of tumor and also the second deadliest cancer. The gut microbiome appears to play a crucial role in carcinogenesis. However, research is still too limited to use microbiota as a clinical screening tool, even though early detection would increase the chances for survival. 

This is why studies published in 2025 in Nature Medicine are so important. They are based on the analysis of 18 datasets: 12 from pre-existing databases including 2,116 individuals (930 patients with CRC, 210 with adenomas and 976 healthy controls) and 6 from new cohorts (1,625 individuals) providing information on both the cancer’s stage and the tumor’s location in the body. In total, the study included 3,741 individuals, providing strong statistical power and potentially accurate results

Species involved, including oral bacteria

The authors detected 3,866 bacterial species, 15 eukaryotes and 23 archaea. The microbiota of healthy controls differ markedly from that of CRC patients, confirming results from previous studies: 125 species are more abundant in patients (106 known and 19 unknown) and 83 in controls (53 known and 30 unknown).

Five subspecies of F. nucleatum were among those more abundant in patients, namely, F. nucleatum subsp. animalis, vincentii (two different subspecies), nucleatum, polymorphum. Other bacteria previously associated with CRC, such as P. micra and B. fragilis, were also identified.

The gut microbiota may be involved in regulating ammonia in the CRC tumor micro-environment.

A significant portion of CRC-specific gut bacteria are typically oral species, with 21 of the 125 species more abundant in patients (16.8%) being oral in origin, including 11 commonly found in dental plaque.

Predicting colorectal cancer

Above all, this large dataset has improved the accuracy of colorectal cancer (CRC) prediction based on a simple stool sample: the area under the curve (AUC), a measure of model performance, now reaches 0.85 —an improvement over previous studies, which achieved a maximum of 0.81. A large part of this predictive power relies on bacteria that are typically oral in origin.

The authors also show that:

• microbial biomarkers are linked to the presence of a tumor,
• they vary according to disease stage: the abundance of P. micra and F. nucleatum increases as early as stage I CRC, while Akkermansia muciniphila and Parabacteroides distasonis rise in advanced stages, suggesting that microbiota changes occur continuously and intensify as cancer progresses (adenoma–carcinoma sequence).
• they also differ depending on tumor’s location: for example, three oral species were significantly more abundant in proximal colorectal cancer.

Previous studies had implicated ammonia in the tumor micro-environment in T-cell depletion and cancer progression.

Rather than “feel good in your skin”, should we be saying “feel good in your skin microbiota ”?

So suggests a British study, linking psychological well-being to the microorganisms living on our skin, specifically the skin of the face, scalp, forearms, and armpits, based on a study of 53 Britons with an average age of 63. This research highlights a system of interactions between the skin and the brain, echoing the now familiar dynamics of the gut-brain axis.

More Cutibacterium, more well-being?

The study shows for the first time an increased abundance of certain bacterial genera in those who feel the best in their skin, both in terms of general well-being and the well-being of the skin area in question. The skin bacterium most common to Britons who feel the most comfortable in their bodies is Cutibacterium (sidenote: Cutibacterium A bacterial genus whose classification has been significantly revised in recent years (until 2016, it was known as Propionibacterium). The genus includes several species, including the infamous C. acnes (an opportunistic pathogen involved in acne and infections of breast implants, shoulders, etc.), as well as C. avidum, C. granulosum, C. namnetense, and C. humerusii Ahle CM, Feidenhansl C, Brüggemann H. Cutibacterium acnes. Trends Microbiol. 2023 Apr;31(4):419-420. ; CTCB ) . Do you have plenty of it on your face? Then you must be fairly stress-free. If your armpits are teeming with it, your mood is likely to be good and your stress levels low. Conversely, a lower abundance of Cutibacterium may contribute to disorders such as stress, anxiety, or depression.

This is somewhat surprising, since Cutibacterium is usually associated with C. acnes and the puberty nightmares that come with it, rather than elderly Britons enjoying their golden years. This bacterium could also promote positive skin health by inhibiting pathogens and regulating skin acidity, thanks to its ability to convert sebum into free fatty acids.

Cause or effect?

The central question is, as always, whether the presence of Cutibacterium is a cause or effect of well-being. In other words, does the presence of Cutibacterium make us happy, or does a cheerful disposition attract Cutibacterium to the skin? Or could it be a third factor common to both, such as lifestyle, exercise, or diet?

At present, we can’t say. We do know that the skin and its microbiota act as a protective barrier for the body, inhibiting pathogens, and thus providing security and peace of mind. Conversely, it has been shown that stress, anxiety, and depression can impact our skin, leading to skin disorders such as eczema (or atopic dermatitis), psoriasis, acne, and underarm odor.

We’ve heard of the gut-brain axis, and now we know there’s a bidirectional skin-brain axis as well, with the former influencing the latter and vice versa. For the first time, a link has been found between skin microbiota and psychological well-being. This should encourage psychodermatology (sidenote: Psychodermatology Psychodermatology is a relatively new field of medicine. It encompasses the interaction of mind and skin. Treatment of psychodermatological disorders focuses on improving function, reducing physical distress, diagnosing and treating depression and anxiety associated with skin disease, managing social isolation and improving patient’s self-esteem. Both pharmacological and psychological interventions are used in treating psychodermatological disorders. Explore Jafferany M, Franca K. Psychodermatology: Basics Concepts. Acta Derm Venereol. … ) research to further study the bacteria involved and their potential influence on our skin and general health.

What do we already know about this subject?

The vaginal microbiota plays a key role in defending against pathogens, maintaining mucosal immunity, and supporting reproductive health. Dominance by Lactobacillus species, especially L. crispatus, maintains a low pH and inhibits pathogenic colonisation² . Dysbiosis — defined by a loss of lactobacilli and overgrowth of anaerobic species such as Gardnerella or Prevotella — is associated with increased risks of bacterial vaginosis (BV), preterm birth³ , infertility⁴, sexually transmitted infections, human papillomavirus (HPV) infections and gynaecological cancers⁵ . Previous studies have shown that hormonal changes, menstruation, and sexual intercourse can influence the composition of the vaginal microbiome⁶. Many of these studies relied on infrequent sampling and lacked resolution to assess short-term fluctuations or determine the drivers of transitions between eubiosis and dysbiosis. The contributions of viral dynamics and functional bacterial genes have remained largely unexplored.

What are the main insights from the study?

This study introduces the concept of VCDs, offering a new framework for classifying microbiome behaviour across the menstrual cycle. Unlike community state types (CSTs), which describe static microbiome compositions, VCDs capture temporal patterns that may better reflect microbiome resilience and vulnerability. The four VCDs — constant eubiotic, constant dysbiotic, menses-related dysbiosis, and unstable dysbiotic — represent distinct profiles of microbial stability. Women in the constant eubiotic group maintained Lactobacillus dominance throughout the cycle, while those with constant dysbiosis had persistent BV-associated communities. Menses-related dysbiosis was characterised by temporary shifts during menstruation, often reverting mid-cycle, whereas the unstable group experienced abrupt fluctuations after exposures like sexual intercourse, suggesting greater ecological fragility.

One of the key findings was that instability in the vaginal microbiome is associated with increased bacteriophage activity and a higher prevalence of L. iners. This species is frequently linked to transitional or less stable states, and phage abundance may reflect active lytic cycles that destabilise dominant bacteria via “kill-the-winner” dynamics. Additionally, women with transient dysbiosis showed increased abundance of potential pathogens such as Sneathia spp. during and after menstruation, pointing to specific periods of vulnerability.

Strain-level analysis revealed differences in bacterial gene content, including bacteriocins produced by Gardnerella leopoldii that may inhibit lactobacilli. These genes were more prevalent in unstable and dysbiotic VCDs, supporting a possible mechanistic role in shaping community structure. Although these genetic findings require further validation, they highlight the importance of moving beyond species-level classification to understand microbial function and its impact on host health.

What are the consequences for clinical practice?

This study underscores the need to rethink how vaginal health is assessed and monitored in clinical practice. The recognition that vaginal microbiota are dynamic — and that stability patterns differ markedly between women — has implications for diagnostics, risk assessment, and therapeutic strategies. Sampling at a single time point, especially during menstruation, may fail to capture meaningful fluctuations or misrepresent a woman’s baseline microbial state. Clinicians should consider collecting samples at multiple points in the cycle to better assess microbiome behavior, particularly in patients with recurrent symptoms or reproductive concerns.

The limitations of CST-based classification are evident in this study. Two women with the same CST may exhibit entirely different VCDs, one with stable eubiosis and the other with frequent dysbiosis. Incorporating VCD assessment could enable more personalised interventions, such as recommending prophylactic microbiome support for women with unstable patterns or targeting high-risk windows (e.g. post-menses) for infection screening.

The identification of phage-driven instability and strain-level bacterial traits opens avenues for precision medicine. Future therapies may need to address microbial function — such as biofilm formation or bacteriocin production — rather than composition alone. Understanding the dynamics of vaginal bacteriophages could also inform novel microbiome stabilisation strategies.

Figure 1. Vaginal time series can be classified into four categories (Vaginal Community Dynamics) according to their proportions of eubiotic samples

a. A decision tree can separate a time series of samples into dynamic groups, based on the community state types (CSTs). Input from the user determines which CSTs are considered eubiotic (here: I, II, and V) and which days are to be considered free from the influence of menses (here: cycle day 9 to cycle day 25). Time series with ≥80% eubiotic samples are considered constant eubiotic; conversely, those with >80% dysbiotic samples are considered constant dysbiotic. For those in the 20–80% range, a second assessment is done on the days free of menses: if they are >80% eubiotic, the time series is considered menses-related dysbiotic, and otherwise unstable (changing from eubiosis to dysbiosis without a clear temporal pattern). b. A colour map with one individual per row and one day per column. The colour of each intersection depicts CST. Coloured bars on the left side show the vaginal community dynamics of each woman. c. Additional colour bars show the inferred vaginal community dynamics of each participant when using fewer samples for classification. Reproduced from Hugerth LW, et al. Microbiome 2024, 12, 1531 (doi:10.1186/s40168- 024-01870-5) under a CC-BY 4.0 license (creativecommons.org/licenses/by/4.0). No changes have been made to the figure.

The classification tool VALODY, designed to assign VCD categories based on VALENCIA CST assignments, is available on GitHub at https://github.com/ctmrbio/valody.

How the menopausal microbiome impacts women’s overall health

Menopause-induced changes lower gut microbiome diversity and cause a shift toward greater similarity to the male gut microbiome. This review details the healthrelated consequences of these changes. During perimenopause, a gradual decline in hormone levels disrupts the gut microbiome balance and contributes to adverse health outcomes, including cardiometabolic disease and changes in oestrogen metabolism. Hormonal fluctuations during menopause change the oral microbiome, heightening the risk for dental caries, periodontitis, and oral infections such as candidiasis. Menopauseinduced vaginal microbiota alterations increase susceptibility to bacterial vaginosis, vulvovaginal atrophy, and recurrent urinary tract infections. Menopause also alters the diversity and abundance of gut microbiota that have been linked to inflammation. Chronic dysbiosis-induced inflammation predisposes menopausal women to metabolic disorders and autoimmune diseases.

This article bridges the gap between endocrinology and microbiology, and emphasises the systemic impact of menopause beyond reproductive health. A key strength of the review is its holistic examination of menopausal-related hormonal fluctuations with corresponding shifts in gut and vaginal microbial composition and diversity. This opens the door to exploring microbiome-based biomarkers for managing menopausal symptoms such as genitourinary syndrome, metabolic changes, or inflammation. This article’s interpretation of age-related changes in women’s health enriches the growing interest in the human microbiome’s role in disease. While hormone replacement therapy has shown promise in mitigating some of the adverse effects of oestrogen deficiency, its broader application is limited by its systemic risks. The targeted use of specific probiotics to restore gut microbial balance, coupled with dietary and lifestyle modifications, may offer safer, more individualised alternatives that mitigate adverse health effects of menopause.

Menopausal microbiome research is overrepresented with data from Western populations and a lack of detailed mechanistic insights. Since diet, lifestyle, and environmental factors significantly influence the microbiome, we need ethnically and geographically diverse research incorporating advanced “omics” approaches to fully elucidate these influences. More effective, personalised treatment strategies will then emerge that can improve the quality of life for menopausal women.

In conclusion, menopause is a whole-body transition involving significant changes in the microbial ecosystem. Understanding and addressing these changes can enhance patient outcomes and promote healthier ageing in women.

Gut microbiota composition in women with polycystic ovary syndrome

The gut microbiota is increasingly viewed as an invisible organ-like system that not only plays an important role in a woman’s wellbeing but also affects the pathophysiology of some disorders such as polycystic ovarian syndrome (PCOS). Knowing about microbial metabolite pathways may elucidate effective treatments.

A recent meta-analysis that included 948 women with PCOS from 14 studies explored the relationships between gut microbiota among women from different regions and with different testosterone levels. Key findings revealed distinct gut microbiota compositions in PCOS patients compared with their healthy counterparts, and significantly different gut microbiota between PCOS patients with higher testosterone levels and those with lower testosterone levels. Also, gut bacterial genera differed among PCOS patients from different regions; European patients had high Alistipes levels, whereas Chinese patients had high Blautia and Roseburia levels.

These findings support current evidence showing that PCOS patients have fewer different types of bacteria and a less balanced microbial community compared with healthy women. The data also confirm the abundance in PCOS patients of specific bacterial genera such as Escherichia/Shigella and Alistipes, which are associated with insulin resistance and inflammation. This study implies that the gut microbiome is linked to various metabolic and hormonal disturbances associated with PCOS, which is compatible with previous research. Importantly, it demonstrates differences in bacterial taxa between Chinese and European women with PCOS, which may assist with personalised treatment strategies. Further research to determine PCOS-associated bacteria strains may enhance anti-PCOS microbial therapies and studies in different geographical regions would promote the global treatment of PCOS.

To conclude, characterising gut microbiota in PCOS patients from different countries may enable gut microbiota to act as a biomarker to distinguish different subtypes of PCOS, and thereby improve the clinical diagnosis and treatment of PCOS.

The role of the vaginal microbiota in women’s health

The human body hosts trillions of microorganisms, collectively known as the microbiome, residing in various locations and coexisting in a complex symbiotic partnership. Importantly, the vaginal microbiota influences women’s reproductive and overall health. Understanding this ecosystem could revolutionise the prevention and treatment of these conditions.

This review highlights the links between dysbiosis of the vaginal microbiota and gynaecological disorders, as well as pregnancy-related complications. Specifically, reductions in lactobacilli and an increased vaginal microbiota diversity are associated with human papillomavirus (HPV) infection, the formation of cervical lesions, and cervical cancer. A loss of vaginal Lactobacillus dominance can create a proinflammatory environment that compromises successful embryonic implantation, leading to infertility. An imbalance in the vaginal microbiome can trigger inflammation leading to pregnancy complications. Having fewer Lactobacillus species in the vaginal microbiome increases the risks of premature rupture of membranes, preterm birth, miscarriage, and ectopic pregnancy. Vaginal dysbiosis may contribute to insulin resistance, a hallmark of gestational diabetes mellitus, and greater diversity in bacterial composition has been found in severe preeclampsia. Testing for Prevotella bivia colonisation during pregnancy may help to predict and mitigate against hypertensive disorders during pregnancy.

This review underscores the key relevance of the vaginal microbiome in women’s reproductive and overall health. The composition of this microbiome can impact everything from fertility and pregnancy outcomes to infection susceptibility. The article covers various aspects of vaginal microbiota, including its relationship with immune system function, inflammation, and pathogen defence, and thereby offers a broad, holistic understanding of its role with generalisable insights into women’s health at large. Enhanced knowledge around how the vaginal microbiome influences health presents an important advance for early disease detection and prevention, instead of treating infections or conditions after they appear. However, long-term study data are needed to clarify the long-term effects of vaginal microbiome imbalances. Moreover, while probiotics and other microbiomebased interventions show promise for maintaining a healthy vaginal microbiome, probiotic strains, dosages, and delivery mechanisms have yet to be standardised for clinical application. Much work remains to be done.

In sum, having fewer vaginal Lactobacillus species and increased vaginal microbial diversity is associated with obstetric and gynaecological complications. This review highlights the possibility of using microbiome-based diagnostics to detect imbalances in vaginal flora, potentially before symptoms manifest. Early intervention may prevent adverse consequences.

Talk about vaginal infections, fertility, or pregnancy complications often focuses solely on women. But there is another important player: the male urogenital tact (MUGT). The wide variety of microbes in the MUGT can significantly affect female reproductive and vaginal health (Figure 1). Understanding these influences may improve outcomes for women, especially those with persistent vaginal infections, fertility challenges, and pregnancy complications.

Figure 1. Consequences of exchanges of bacteria associated with vaginosis during sexual contact between males and female

What do we know about the male genital microbiota?

The MUGT includes several distinct microbial environments: the skin of the penis, the urethra, semen, and the urinary tract. Each has a unique bacterial community, influenced by factors like circumcision, sexual practices, hygiene, and lifestyle.

MUGT microbiota vary with circumcision status, sexual practices, and the composition of the female partner’s vaginal microbiota⁷.
Interestingly, the urethral microbiota of homosexual men does not seem to be modified by the type of sexual intercourse (oral or anal)⁸. Bacterial exchanges between partners during sexual contact are the rule; why these exchanges lead to vaginal dysbiosis in some cases and not others is unclear.

Seminal microbiota are also influenced by several physiological functions (age, hormonal changes) and lifestyle or epigenetic factors
(tobacco, alcohol, obesity, high-fat diet, exposure to toxins)⁵. These modifiable factors are potential targets for intervention.

How does the MUGT impact female health?

The transmission of microorganisms responsible for bacterial and viral sexually transmitted infections (STIs) including HIV and herpes simplex virus infection during sexual contact is the most obvious consequence of how the MUGT impacts female health. The female complications of bacterial STIs (gonorrhoea, infections by Chlamydia trachomatis or M. genitalium) are well known (inflammation and infection of the upper genital tract, risk of tubal infertility).

Many studies have shown that the epidemiological profile of women with BV is comparable to that of women with STIs, suggesting possible sexual transmission of the bacteria involved in BV. The presence of BV-associated bacteria in the foreskin and urethra of partners of women with BV and a concordance of vaginal and male urethral bacterial strains support the sharing of these strains or sexual transmission of BV.

Treating the male partner with oral antibiotics (metronidazole) has had very limited impact on recurrence rates in women with recurrent
BV, although combining metronidazole with a topical antibiotic applied to penile skin in partners of women with BV may reduce the risk of recurrence⁹.

The impact of the MUGT on uterovaginal health is not limited to passive bacterial transfer. Seminal fluid contains proinflammatory substances (such as prostaglandins) that can interfere with immune responses and inflammation within the female genital tract¹⁰.