Recurring BV? Your Partner’s Microbiome Might Be the Missing Link

If you’ve ever found yourself stuck in a frustrating cycle of bacterial vaginosis (BV) that just won’t shift, you’re not alone. For many women, BV becomes a revolving door of symptoms and unfortunately with a lack of understanding around the drivers to this condition and inaccurate testing, recurrent infection is extremely common.

There is something that may be contributing to your issues that you haven't yet thought of!

Recent research is shedding light on an important factor that is very commonly missed: your partner’s reproductive microbiome may be silently influencing yours. This 2022 study discussing the role of the reproductive microbiome for fertility health, quite clearly maps out the impact:

“Unprotected sexual intercourse creates a bacterial exchange between partners, and in addition, each partner can influence the microbiota composition of partner's reproductive health tracts” (Koedooder et al., 2022).

If BV keeps coming back, it's time to consider not just your treatment, but the shared microbial environment between you and your partner.

Vaginal Microbiome 101: Why Balance Matters for Recurring BV

The vaginal microbiome is best described as a low-diversity ecosystem typically dominated (in a healthy state) by a single Lactobacillus species. That dominant bacterium keeps the pH acidic and suppresses other microbes. When this dominance is lost (dysbiosis), anaerobes or fungal species can overgrow, raising the risk of bacterial vaginosis, yeast infections, and greater susceptibility to STIs.

Many factors can tip this balance. Changes in hormone levels throughout the menstrual cycle, personal hygiene practices, diet and lifestyle and medications such as antibiotics or the contraceptive pill are common examples. In addition, the transfer of microbes between partners during intimate contact can significantly affect vaginal health.

The Microbial Exchange Between Partners

Sexual partners share more than intimacy, they share microbiomes. Whether in heterosexual or same-sex relationships, the reproductive microbiota can shift through unprotected intercourse. That means one partner’s bacterial landscape can directly influence the other’s, sometimes in ways that make treatment for vaginal dysbiosis frustratingly ineffective.

So, when only one person is treated, it’s a bit like patching a leak without checking the rest of the plumbing.

What a Partner-Inclusive Approach Looks Like

Shifting our lens from “treating a woman’s infection” to “addressing a couple’s shared microbiome” opens up more effective pathways for care:

• Testing Both Partners - Assessing microbiota from both individuals can identify patterns that might otherwise go unnoticed, like a male partner carrying BV-associated bacteria that reintroduce imbalance after treatment.

• Treating in Tandem - Simultaneous treatment (e.g. antibiotics, probiotics, or lifestyle shifts) reduces reinfection risks and creates space for long-term microbiome restoration.

• Preventative Conversations - Encouraging partners to talk about sexual health, microbiome balance, and the impact of behaviours like condom use, hygiene, and even diet fosters a proactive approach to wellbeing, not just reaction to symptoms.

  
  

The Hidden Consequences: Endometriosis, Infertility & Recurrent Pregnancy Loss

The impact of vaginal dysbiosis has much broader implications for reproductive health. Particularly for women. Overgrowth of certain microbes and a lack of beneficial lactobacillus species has been shown to lead the way to a pro-inflammatory environment. Setting the stage for an increased risk in conditions like endometriosis, infertility and recurrent pregnancy loss.

Endometriosis: A positive correlation exists between vaginal microecology dysbiosis and endometriosis, notably with intermediate BV (Wang et al., 2024).

Recurrent Pregnancy Loss (RPL): BV has also been shown to be significantly associated with spontaneous abortion in a large meta-analysis including over 20,000 women (Haahr et al., 2016).

Assessment of the vaginal microbiome in addressing all aspects of women's menstrual and fertility health is an essential consideration.

Vaginal Microbiome Testing: Gram Stain, PCR, and NGS Explained

When it comes to vaginal health, there are a few ways your microbiome can be tested, some more beneficial than others. Here’s a quick look at the main methods:

1. Gram-Stained Vaginal Smear (Hay/Ison)

This is the test most people are familiar with.Your GP takes a vaginal swab, sends it to the lab, and technicians stain it so bacteria are visible under a microscope.They then grade what they see using the Hay/Ison criteria, which helps diagnose bacterial vaginosis (BV) or assess your overall flora balance.

It’s quick, inexpensive, and great for spotting obvious infections, but it only gives a broad overview of what’s happening.

In short: It shows whether Lactobacillus (the “good” bacteria) are dominant or if other bacteria have taken over, but it doesn’t tell you exactly which species are present.

2. PCR Test

PCR looks for the DNA of specific microbes in your sample. It’s mostly used to check for STIs or targeted bacteria. It looks for the genetic material (DNA or RNA) of specific pathogens (for example, Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, or Mycoplasma genitalium).

PCR gives species-level information but is usually used for infections, not general microbiome screening on the NHS.

3. Next-Generation Sequencing (NGS)

NGS is a more advanced, DNA-based test. Instead of looking at bacteria under a microscope, it reads the genetic code of all the microbes in your sample. This means it can identify hundreds of bacterial species, including ones that can’t be seen or cultured in a standard lab test.

NGS can also detect subtle shifts in your microbiome, changes that may not cause symptoms yet but could affect fertility, pregnancy outcomes, or vaginal health over time.

It’s the test researchers often use to explore conditions like endometriosis and recurrent pregnancy loss, where microbial balance may play a role. This is the preferred test for Functional Medicine practitioners based on its specificity and reliability.

Side-by-Side Comparison of Vaginal Microbiome Tests

Feature	Gram-Stained Smear (Hay/Ison)	PCR Test	Next-Generation Sequencing (NGS)
Used by NHS?	Yes - standard for BV	Yes - mainly for STIs	No -research/private only
Method	Microscopy	DNA amplification	Whole-genome or 16S rRNA sequencing
What it detects	Bacterial morphotypes (Lactobacillus vs BV bacteria)	Specific microbial DNA (targeted)	Full microbial community profile
Level of detail	Low	Moderate (species-specific if targeted)	Very high (species-level + abundance)
Common uses	Diagnose BV, assess flora	Detect STIs, specific BV/STI panels	Research, fertility, chronic dysbiosis
Speed	Hours	Hours–1 day	Days–weeks
Cost	Low	Moderate	High
Availability	Routine GP/sexual health clinics	NHS for STIs, private for microbiome	Specialist labs/private clinics

What About Testing for Men?

So we’ve established the testing options for women, but the point of this blog is about shared microbes between partners. So how do we go about testing men?

Testing can be done with a swab from the urethra, penis, or foreskin. This is similar to the Gram-stained smear used in women, but it’s less commonly performed in men.

It only shows broad bacterial groups and can’t identify specific species.

A PCR test can also be performed and is the most commonly used test for detecting viruses or STIs in men. PCR detects DNA from specific bacteria, such as Chlamydia, Gonorrhoea, or Mycoplasma. The sample is usually a swab, but it can sometimes be done with a first-catch urine sample. PCR is very accurate for targeted infections, but it doesn’t provide a full picture of the microbiome - it only tests for known pathogens.

Next-Generation Sequencing (NGS) can analyse the entire male genital microbiome, including bacteria, viruses, and fungi. It’s mainly used in research or private fertility clinics.

Pros: Very detailed; can detect subtle microbial imbalances that may affect fertility.

Cons: Expensive, slower, and not routine in NHS clinics.

NGS can also be performed on semen to look at the bacteria and other microbes in a man’s reproductive system. A semen sample is collected in a sterile container, and the DNA of all microbes is analysed. This gives a detailed picture of the microbial community and can help fertility specialists understand possible links between microbes and sperm health or unexplained infertility. NGS doesn’t test sperm directly, and it’s not a routine NHS test, it’s mainly used in private clinics or research studies.

Because of its specificity and accuracy, NGS is the preferred test by Functional Medicine practitioners. It helps identify potential drivers of male factor infertility and inflammatory microbes that may negatively impact sperm quality. Importantly, it’s also the best way to address dysbiosis that may be shared between partners, which can create a cycle of reinfection and impact both reproductive microbiomes. When recurring BV is an issue both partners must be tested.

A Call for More Inclusive, Evidence-Based Care

It’s time to evolve how we approach vaginal health. The one-sided treatment model doesn't reflect the science or the lived experiences of so many women dealing with persistent, recurrent BV. A shared microbiome requires a shared strategy, one that includes both partners in the conversation, the testing, and the treatment plan.

How Can I Do This?

When it comes to addressing recurrent BV, I always test both my clients and their partners - this is a private Next-Generation Sequencing (NGS) test that you can do from the comfort of your home. If needed, I work alongside medical treatment and provide guidance on how to access it.

While antibiotics can be helpful, using them alone often leads to reinfection. That’s why a comprehensive approach is better, one that focuses on nutrients and herbs to help break down microbial biofilms, making bacteria more susceptible to antibiotics, while also implementing long-term strategies to rebuild a healthy vaginal pH, support Lactobacillus species, and address other contributing factors such as hormonal balance, gut health, and immune system support.

If you would like to break the cycle of recurrent BV and take control of your vaginal and reproductive health, book a consultation to explore testing options for you and your partner, and discover a personalised plan to restore balance, prevent reinfections, and support long-term wellness.

Book a Free Discovery Call

References

Koedooder, R., Singer, M., Schoenmakers, S., Savelkoul, P. H. M., Morré, S. A., de Jonge, J. D., & Broekmans, F. J. (2022). The role of the reproductive tract microbiome in reproductive health: A review. Frontiers in Cellular and Infection Microbiology, 12, 909853. https://doi.org/10.3389/fcimb.2022.909853

Wang, X., Xu, X., Zhang, X., et al. (2024). Association between vaginal microbiota dysbiosis and endometriosis: A cross-sectional study. PLOS ONE, 19(8), e0306780. https://doi.org/10.1371/journal.pone.0306780

Haahr, T., Ersbøll, A. S., Karlsen, M. A., et al. (2016). Bacterial vaginosis and spontaneous abortion: A meta-analysis. Journal of Human Reproductive Sciences, 9(4), 221–228. https://doi.org/10.4103/0970-9371.188050