In Part I we explored the fascinating reasons why minding your gut microbiome is important for balancing hormones and optimizing fertility. More specifically, I explained how the estrobolome, the aggregate of bacteria in the gastrointestinal tract, directly impacts hormonal health through its role in metabolizing estrogens. (source, source, source, source)

This may have come as a surprise to many, but the relief that the same actions that benefit the overall microbiome also supports the estrobolome makes life a bit simpler. These include eating nurturing food, allowing for rest, connecting to loved ones, moving the body, and eating fibers and veggies.* (source, source, source, source)

In this post, I will discuss a second aspect related to endocrine health most people don’t consider. It is connected to keeping our belly bugs happy for overall hormonal health. It is your reproductive microbiome.

Why You Need to Know About Your Reproductive Microbiome

Now that we are becoming more aware of how essential the gut microbiome is to overall health (source), scientists are also validating the benefits of being unsterile in every nook and cranny of, on, (source, source, source, source) and around our body.

The benefits of organisms in our reproductive tract is one area that is currently being explored. It is a new and emerging field and is very complex. According to a 2020 article in Trends in Ecology and Evolution, “In the broadest sense, the reproductive microbiome can be defined operationally as the microbiome, including bacteria, viruses and unicellular algae, protozoans and fungi, living in or on any structure, organ, fluid, or tissue of a host that typically makes contact with the gametes (or gamete analogues, e.g., pollen or gametophytes) or reproductive tract or organs of another individual through mating, spawning, or pollination.”

At the recent naturopathic medicine conference, Dr. Chase provided a complete review of what we know at this point on this topic. She provided enough references to keep me occupied for the rest of the year.

Below, I review some of the key points I learned from her exceptional presentation and some of the latest research.

The Vaginal Microbiome

The vaginal microbiome is a hot topic in the “-omics” and reproductive health revolution. According to Holistic Primary Care, “Recently, Virginia Commonwealth University launched a major research initiative called the Vaginal Microbiome Consortium, to foster cross-disciplinary studies on the vaginal flora and how it influences women’s health, sexuality, fertility, and infant health and well-being.”

Dr. Chase explained how the healthy vaginal microbiome is populated with a predominance of lactobacilli, which produces protective lactic acid for acidification. This functions to keep unwanted microbes at bay. For this reason, it is important to not to introduce harsh feminine hygiene products that could disturb this delicate microbial population.

Just as every gut microbiome has its unique genetic “fingerprint,” various factors contribute to variations in species in the vaginal microbiome. These include ethnicity and estrogen levels. (source)

A new study recently confirmed the connection of the vaginal microbiome to hormonal levels. The results indicated a correlation between women on hormone replacement therapy (HRT) and higher levels of lactobacilli in their urine. Those on HRT had a lower risk of urinary tract infection (UTI) as a result of consistent estrogen availability. This doesn’t mean that we should be using HRT for UTIs, but it does confirm the relationship between balanced hormones and healthy vaginal and urinary flora. Health Day reported on the results:

“Estrogen stimulates our vaginal cells to produce more of these kinds of carbohydrates that Lactobacilli really like to eat,” De Nisco said, describing one theory why hormone therapy might promote healthy vaginal bacteria. “Basically, estrogen makes our cells make more food for the Lactobacilli,” she explained.


Keeping Your Vaginal Microbiome Balanced

Things that disturb the vaginal microbiota include douching, stress, smoking, dietary factors, having a high number of sexual partners without proper precautions, and improper hygiene. These should all be considered for a healthy vaginal microbiome.

For my clients that struggle with chronic vaginal infections and hormonal balance, ensuring optimization of gut health and nourishing supportive lifestyle factors has also been very helpful for relieving complaints related to discomfort during sex, vaginal dryness, yeast infections, and urinary frequency. Specific probiotic strains have been found to decrease inflammation in the vagina and restore balance of the lactobacillus species. I have used several in my practice, along with many other personalized recommendations for each unique woman. (source)

The Reproductive Microbiome: Ovarian and Uterine Microbiome

The endometrial microbiome provides various immune functions and it also shifts with menstrual cycles and hormonal fluctuations. Predominance of certain microbes based on hormonal balance can influence implantation and pregnancy outcomes.


Tips for a Healthy Ovarian and Uterine Microbiome

It is important to keep systemic inflammation down through the lifestyle factors discussed above. Those struggling with fertility may want to pay extra attention to what microbes they are feeding with diet and probiotic supplementation. For example, if the endometrium is dominated by Bacteriodies, improved implantation rates occur. If it is dominated by Lactobacillus there are better pregnancy outcomes. Furthermore, dysbiosis in the reproductive microbiome can negatively impact pregnancy outcomes.




Placental Microbiome & Pregnancy

The baby is not sterile in the womb. The hormone fluctuations of pregnancy that influence mom’s microbiota and pregnancy outcomes also impact her baby’s microbiota. For example, progesterone has been shown to increase Bifidobacterium in the mother’s gut.

Interestingly, the mom’s oral microbiota is most similar to the placental microbiome. This means oral care should be optimized prior to pregnancy.

By the third trimester, the baby’s gut microbiome is most associated with mom’s diet. This may be why probiotics have been shown to be helpful in pregnancy for certain outcomes, but results have been mixed regarding other outcomes related to fertility. (see above) (source, source, source, source)


Applications for Moms-to-Be

Moms-to-be should pay extra attention to their dental care prior to pregnancy. Throughout pregnancy, they should include nourishing, tasty foods to feed their own and baby’s microbiome


For the Guys: The Semen Microbiome

According to Dr. Chase:

Semen contains nutrients, microbes (healthy & unhealthy), amino acids, and more. Semen is also a form of elimination of what the man is exposed to. (source)


Tips to Support Healthy Semen

  1. Encourage men to eliminate through all channels of detoxification (bowels, sweat, hydration, urination)
  2. Ensure proper hydration
  3. Ensure a healthy gut to support elimination



Although the subject is complex, the applications of nurturing your body and mind to support your reproductive microbiome aren’t that complicated.

Factors that have been linked to estrogen levels in the body, and potentially impact the estrobolome and reproductive microbiome include: antibiotic use, diet, alcohol, exercise, stress, xenoestrogens (environmental exposures), and probiotics. (source, source, source) These are all things that you can control to keep your estrobolome and reproductive microbiome healthy and happy.


Let me hear your thoughts below.

Comment below. 🙂


Note: “Women” is being used to refer to any -cis, -trans, or “they” that has any reproductive organs conventionally viewed as “female sex” in the medical literature. I am aware that this terminology is shifting, and I will do my utmost to understand and appreciate that fact.

*Check with your naturopathic or functional medicine doctor for a personalized nutrition plan, especially if you are sensitive to “healthy” foods and fibers.

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