How microbiome-focused fertility care can support women with PCOS trying to conceive

 A guest blog authored by Julia Young, Registered Nutritional Therapist & Fertility Specialist
 

Many women with PCOS follow all the advice they’re given, only to be told that their tests look “normal” or that there is no clear explanation for why conception isn’t happening. For some others, conception occurs but is followed by early pregnancy loss without an obvious cause. As a fertility nutritionist specialising in PCOS, I see this situation all the time. One of the most important lessons I’ve learned is that PCOS-related fertility challenges are rarely explained by one factor alone. They are multi-layered, and the vaginal microbiome is an area that is often overlooked.

Why the vaginal microbiome matters in PCOS

The vaginal microbiome is a delicate ecosystem made up of bacteria and microbes that help maintain an environment favourable for conception and early pregnancy. A stable, Lactobacillus-dominant microbiome supports implantation, protects against infection and 
helps maintain the acidic pH that discourages pathogenic bacteria. However, many women with PCOS experience disruptions in this microbial balance, even when they have no symptoms at all. Research has shown that women with PCOS may be more likely to carry a higher abundance of pathogenic or inflammatory bacterial species, as well as having lower levels of protective Lactobacillus. These imbalances (known as vaginal dysbiosis) have been linked to:

 • Reduced implantation rates
 • Higher miscarriage risk
 • Increased likelihood of preterm birth
 • Greater susceptibility to infections, including those that may be silent

This is why, in my practice, vaginal microbiome testing is an essential part of building a complete picture of fertility health for clients with PCOS.

Why women with PCOS may be at higher risk

PCOS is often described as a reproductive and metabolic condition, but its impact reaches further than hormones and ovulation. Several core features of PCOS can help explain why miscarriage risk is higher, and why identifying vaginal microbiome imbalances before trying to conceive is so valuable.

1. Insulin resistance


Many women with PCOS experience some degree of insulin resistance. This can influence egg quality, endometrial development and early embryo health, increasing the risk of pregnancy complications. Insulin resistance is also associated with systemic inflammation, an environment in which pathogenic, inflammatory vaginal microbes may be more likely to thrive.

2. Hormonal imbalances


PCOS is characterised by higher androgens and disrupted progesterone patterns. These hormonal shifts can affect immune regulation within the reproductive tract, making it harder for the vaginal microbiome to maintain stability. Even subtle imbalances may change the pH of the vagina, creating an opportunity for pathogenic bacteria to overgrow.

3. Higher rates of obesity


Not all women with PCOS live in larger bodies, but for those who do, weight-related inflammation and metabolic stress may further increase the risk of miscarriage and other complications. There is also evidence that obesity itself can alter the composition of the vaginal microbiome. These factors help explain why women with PCOS may be more vulnerable to the types of microbial disturbances that are known to affect implantation, pregnancy maintenance and 
overall reproductive wellbeing.

The case for testing, even without symptoms

A common misconception is that vaginal microbiome issues always cause clear symptoms such as odour, discharge or discomfort. In reality, many women with PCOS and underlying dysbiosis feel completely well. This is particularly true for low-grade infections or shifts in microbial balance that affect fertility but don't cause typical signs of Bacterial Vaginosis or thrush.

For this reason, I routinely recommend vaginal microbiome testing for clients with PCOS who are trying to conceive, whether naturally or with assisted reproduction. It allows us to:

 • Identify pathogenic bacteria such as Bacterial Vaginosis associated bacteria or Ureaplasma

 • Assess levels of protective Lactobacillus species

 • Understand whether inflammation or pH imbalance may be impacting implantation

 • Rule out underlying microbial contributors to recurrent miscarriage

 • Create a targeted plan to improve the reproductive environment before conceiving

Testing provides clarity, allowing us to intervene effectively rather than guessing.

The positive news: there is so much that can be supported

Although the microbiome can be disrupted in PCOS, it is also highly responsive to diet, lifestyle and targeted interventions. With the right approach, the vaginal microbiome can shift towards a more protective, pregnancy-friendly state, this is one of the reasons I love integrating microbiome work into PCOS fertility care.

About the Author

Julia runs a clinic working closely with individuals and couples trying to conceive, with a special focus on supporting women with PCOS.

Her approach combines comprehensive assessment, including vaginal microbiome testing where appropriate, with personalised 
nutrition, targeted supplementation and lifestyle strategies that address the root causes of fertility challenges.

Julia runs an online group programme, PCOS To Pregnancy, which helps women with PCOS optimise their fertility in a structured, supportive environment.

To download Julia’s free guide: The 3 Hidden PCOS Mistakes Keeping You From Conceiving, visit https: Free PCOS Guide

Find out more here: Julia Young Nutrition

References

Jin C., Qin L., Liu Z., Li X., Gao X., Cao Y., et al. Comparative analysis of the vaginal microbiome of healthy and polycystic ovary syndrome women: a large cross-sectional study. Reprod Biomed Online. 2023 Jun;46 (6):1005-1016. doi: 10.1016/j.rbmo.2023.02.002. 
PMID: 37085428.

Association of Polycystic Ovarian Syndrome (PCOS) With Vaginal Microbiome Dysbiosis: A Scoping Review. 2024. PMID: 39027755.

Gut and Vaginal Microbiomes in PCOS: Implications for Women’s Health. 2022. PMID: 35282446.