The Gut and Reproductive Microbiome: What You Really Need to Know for Your Fertility
When you think about fertility, your gut might not be the first thing that comes to mind. But new research is showing just how much your gut and the trillions of microbes living in it can affect your hormones, immune system, and even your chances of getting and staying pregnant.
And it’s not just your gut. Your vaginal and uterine microbiomes also play a huge role in your reproductive health.
In this article, we’re exploring what the gut and reproductive microbiomes actually are, how they influence fertility and reproductive health, and what you can do to support them through diet and lifestyle.
What Is the Gut Microbiome and Why Does It Matter for Fertility?
Your gut microbiome is made up of trillions of bacteria, fungi and other microbes that live in your digestive tract. These tiny organisms do big jobs, like:
- Supporting digestion and bowel regularity
- Helping you absorb nutrients like iron, zinc, folate and vitamin B12
- Producing helpful compounds (like short-chain fatty acids) which improve bowel health
- Regulating your immune system
A healthy gut microbiome is diverse, meaning it includes a wide range of beneficial bacteria. Our gut microbiome is as unique as our fingerprint, meaning there is no “normal” that everyone should be striving for, but their own unique “normal”. This makes it challenging to test or assess how healthy an individual’s gut microbiome is on a detailed scale, as we don’t have an accurate reference to compare it to.
More on our gut microbiome here: The Gut Microbiome: From pre-conception to childhood
The Gut-Hormone Axis
Did you know your gut helps regulate your oestrogen levels?
A group of gut bacteria known as the estrobolome plays an important role in processing estrogen and helping to keep your levels balanced.
How Can the Gut/Estrobolome Affect Reproductive Conditions Like Endometriosis and PCOS?
PCOS:
A mini-review of studies from 2016 to 2020 found that people with PCOS tend to have an altered gut microbiome, regardless of body size. The research, which included both human and animal studies, showed reduced bacterial diversity and shifts in specific bacterial strains that may impact metabolism and hormone regulation. These gut changes could play a role in the development or severity of PCOS symptoms. In addition, one study found that 42% of those with PCOS also experienced IBS symptoms.
Read more here: Could Your Gut Microbiome Be Affecting PCOS?
Endometriosis:
Emerging research suggests that gut health may play a key role in endometriosis. Studies have found that people with endometriosis often have a unique gut microbiome “signature” – meaning the balance of bacteria in their gut looks noticeably different compared to those without the condition. An imbalanced gut microbiome can also affect the estrobolome (the group of gut bacteria involved in processing oestrogen), potentially leading to higher circulating oestrogen levels. Over time, this can contribute to the development and progression of endometriosis, making gut health an important – and often overlooked – piece of the puzzle. The research in this area is still new and ever evolving so stay tuned!
What about the endometriosis and IBS link? Similarly to PCOS, many people with endometriosis also report experiencing IBS-like symptoms. In fact, one study found that up to 52% of women who had endo also reported having IBS symptoms.
What About the Vaginal and Uterine Microbiomes?
Unlike the gut microbiome, the vaginal microbiota is considered healthy when it is almost exclusively populated (>90%) by Lactobacilli.
Let’s bust a myth: the uterus is not sterile. BUT it is less concentrated in microbes (100-10,000 times lower bacterial load) and is distinctly different from the vagina
The microbiota in both areas help regulate inflammation and immunity around conception and implantation. Lactobacillus crispatus: most linked to benefits for fertility and IVF & pregnancy outcomes too – look for this when supplementing probiotics.
The Cross-Talk Between Gut and Reproductive Microbiome
Your gut and vaginal microbiomes don’t work in isolation; they communicate with each other more than we ever previously thought.
A 2020 study found that the gut acts as a reservoir for vaginal bacteria, disturbances in gut microbiota may influence vaginal microbiota composition and local immune responses, thereby affecting gynaecological and reproductive health.
A 2025 study found that even when someone had a poor vaginal microbiome, if their gut microbiome was healthy this can dampen inflammation at the local cervicovaginal level – huge win for those navigating implantation concerns.
Translation? Supporting your gut health may help protect your reproductive tract and improve fertility outcomes.
When the Reproductive Microbiome Is Out of Balance
Here are some common disruptors and what they mean:
- Candida albicans – responsible for thrush
- Bacterial Vaginosis (BV) – a common imbalance that can be sexually transmitted and linked to miscarriage, implantation failure, and preterm birth.
- Ureaplasma urealyticum – associated with fertility issues in both men and women.
Symptoms like discharge, odour, frequent thrush or vaginal discomfort may be signs that your vaginal microbiome needs support.
Should You Get Reproductive Microbiome Testing?
It’s still an emerging space, but testing with an EMMA or ALICE test may be helpful if you’re dealing with:
- Recurrent implantation failure (2+ embryo transfers without success)
- Unexplained infertility
- Recurrent pregnancy loss (2 or more consecutive pregnancy losses)
Diet Strategies to Support Your Gut, Vaginal and Uterine Microbiomes
Here are evidence-backed dietary tips to support both your gut and reproductive microbiomes. These strategies may also help ease IBS symptoms, although individualised support is often needed for best results:
Eat 30+ different plant foods each week
Fruits, vegetables, nuts, seeds, wholegrains, legumes and beans and even herbs & spices count!
Fibre diversity helps promote diverse, beneficial bacteria in the gut microbiome, and bonus – keeps your digestion ticking along nicely too!
Limit highly processed foods
Reduce takeaway, sugary drinks, alcohol, and ultra-processed snacks.
Boost polyphenols and antioxidants
Think berries, olive oil, colourful veggies, green tea, and dark chocolate.
Try fermented and prebiotic-rich foods (as tolerated)
Some ideas to try it out include yoghurt, kefir, miso, sauerkraut, garlic, onion, leeks, oats, and legumes like lentils or chickpeas.
If you have IBS or food sensitivities, work with a dietitian to personalise your plan.
Probiotics
Research shows that oral probiotics can improve the vaginal microbiome indirectly – and in some cases, they’re just as effective as vaginal probiotics for treating things like BV (bacterial vaginosis).
When choosing a probiotic, look for strains like: Lactobacillus crispatus – best for fertility and pregnancy
Read more here: The Best Probiotics for Fertility: How Gut & Vaginal Health Impact Conception
Want Personalised Help Supporting Your Miccrobiome?
Whether you’re trying naturally or preparing for IVF, we can help you assess your gut and reproductive health and create a plan tailored to you. Book a Fertility Nutrition Intensive or Learn more about Nutrition Coaching with our Australian Fertility Dietitians Here.
We’re here to help you feel informed, empowered, and supported – every step of the way.
