The Vaginal Microbiome & Reproductive Health: What Every Woman Should Know

When we think about reproductive health, conditions like endometriosis or PCOS are often viewed only through the lens of hormones alone. But what’s often overlooked is the role of the vaginal microbiome, the community of bacteria and microorganisms that live within the vaginal environment.

Just as the gut microbiome influences digestion, immunity, and mental health, the vaginal microbiome plays a central role in fertility, cycle health, and even how conditions like endometriosis and PCOS present in the body.

The Vaginal Microbiome & Reproductive Conditions

A healthy vaginal microbiome is typically dominated by Lactobacillus species. These bacteria keep the vaginal pH slightly acidic, helping to protect against pathogens and inflammation. But when this balance is disrupted, it can ripple out into the whole reproductive system:

• Endometriosis: Research suggests women with endometriosis often have reduced Lactobacillus and higher levels of opportunistic microbes. This imbalance can worsen inflammation, increase pain sensitivity, and contribute to immune dysfunction that fuels endometriosis progression.
• PCOS (Polycystic Ovary Syndrome): PCOS is strongly tied to metabolic and inflammatory pathways. Dysbiosis in the vaginal microbiome has been linked with higher rates of bacterial vaginosis, recurrent infections, and systemic inflammation, all of which may worsen PCOS symptoms or fertility struggles.

Hexa-LPS is an endotoxin produced by certain bacteria such as E.coli, Prevotella species such as P. bivia and P. disiens, Gardnerella vaginalis, Atopobium vaginae, Porphyromonas asaccharolytica, and Mobiluncus species has been found in menstrual blood & ovarian tissue, indicating a broader involvement in reproductive health.

In both conditions, the vaginal microbiome acts as a signal system. When balanced, it supports cycle health, fertility, and comfort. When disrupted, it can add another layer of stress to an already sensitive reproductive system.

Gentle Ways to Support Your Vaginal Microbiome

Supporting the vaginal microbiome isn’t about “quick fixes.” It’s about creating an environment where protective bacteria can thrive and inflammation is kept at bay. Some intentional practices include:

• Choose breathable underwear: Synthetic fabrics trap moisture and heat, which can disrupt pH and encourage overgrowth of harmful bacteria. Opting for organic bamboo underwear is a simple switch that allows the skin to breathe, keeps the area cooler, and reduces irritation.
• Nourish your gut microbiome: Since the gut and vaginal microbiomes are connected, supporting gut health with diverse plant fibres, prebiotics, and probiotics also nurtures the vaginal environment.
• Avoid harsh washes and douches: The vagina is self-cleaning. Over-cleansing with fragranced products can strip away protective bacteria and alter pH balance. Warm water is enough.
• Support your immune system: Chronic stress, lack of sleep, and nutrient deficiencies weaken immune defences, allowing dysbiosis to take hold. Simple lifestyle practices—mindful movement, restorative sleep, and balanced meals—help maintain microbial resilience.
• Cycle awareness: Tracking symptoms around your cycle can help you identify patterns where microbiome imbalance is more likely (for example, post-antibiotic use, during luteal phase spotting, or after stressful periods). This awareness can guide when to be extra supportive with probiotics or soothing self-care.

Your vaginal microbiome is more than just “bacteria.” It’s an essential part of your reproductive ecosystem, influencing inflammation, immunity, and fertility. When you tend to it with simple, mindful practices, like choosing breathable fabrics, honouring your gut health, and lowering stress. You create conditions that support not only your vaginal health but also your whole hormonal and reproductive wellbeing.

When living with conditions like endometriosis or PCOS, this can become a powerful piece of the puzzle; helping reduce flare-ups, improve comfort, and build resilience from the inside out.

Guest post written by Stephanie Pacheco-Nunes of Eclipse Wellness; degree qualified Naturopath & Reiki practitioner

See more from Stephanie at @eclipse_naturopathy & www.eclipsewellness.com.au