For most of my life I thought about the microbiome as one thing. The gut. You eat yogurt, you take a probiotic, you look after your gut bacteria. That was the extent of it.
Then I started doing the kind of deep research that perimenopause forces you into when nothing you try seems to be working the way it should. And I kept coming across something that genuinely changed how I think about my health: the body does not have one microbiome. It has many.
Your gut is just one of them. And when estrogen declines in perimenopause and post-menopause, every single one of them is affected.
You Are More Microbe Than Human
Scientists estimate there are at least as many microbial cells in and on your body as there are human cells. These microbial communities live in dozens of locations throughout your body, each with its own specific population of bacteria, fungi, and other microorganisms that perform distinct roles in keeping you healthy.
The seven primary microbiome sites in the human body are your gut, your skin, your mouth and oral cavity, your lungs and respiratory tract, your eyes, your urinary tract, and your reproductive system. Each one is a separate ecosystem. Each one can be in balance or out of balance. And each one communicates with the others.
"When I learned that my body had microbiomes in places I had never even thought about, the list of symptoms I had been writing off as just menopause started to make a lot more sense."
What Estrogen Has to Do With All of This
Estrogen is not just a reproductive hormone. It plays a regulatory role across multiple body systems, including the health and diversity of your microbiomes. When estrogen is present in healthy levels, it actively supports microbial diversity throughout the body. When it declines, as it does throughout perimenopause and drops sharply in post-menopause, the impact reaches well beyond your reproductive system.
Research has established that estrogen helps maintain the integrity of the gut lining, supports the diversity of vaginal bacteria, influences the bacterial populations on your skin, and plays a role in oral microbiome balance. A 2025 review published in Frontiers in Endocrinology confirmed the bidirectional relationship between gut microbiota and estrogen, showing that the gut microbiota and estrogen actively regulate each other, and that disruptions in this relationship directly influence menopausal health outcomes.
For a deeper look at how your gut microbiome specifically interacts with your hormones, including the estrobolome and how your gut bacteria actually regulate estrogen levels, my article on the gut-hormone connection covers that in full.
Each Microbiome, What It Does, and What Changes
The most researched and the one most people know about. Your gut bacteria regulate digestion, produce short-chain fatty acids that feed the gut lining, influence immune function, and through the estrobolome, help metabolize and recirculate estrogen. A large-scale survey cited in the 2025 Frontiers review found that gut microbiome diversity is measurably lower after menopause, and this reduced diversity is linked to worsening symptoms including weight gain, inflammation, and cognitive changes.
Healthy vaginal flora is dominated by Lactobacillus species, which maintain an acidic pH that protects against infection. Estrogen directly supports Lactobacillus populations. As estrogen declines, this protective balance shifts, which is why vaginal dryness, discomfort, and recurrent infections become more common in perimenopause and post-menopause. This is a microbiome problem as much as a hormonal one.
The urinary tract has its own microbial ecosystem closely connected to the vaginal microbiome. Changes in vaginal flora can affect urinary microbiome balance, which is one reason urinary tract infections become more frequent for many women after menopause. Supporting the vaginal microbiome also supports urinary health.
Hormonal changes in menopause are associated with increased gum sensitivity and higher rates of gum disease. The oral microbiome regulates the bacterial balance in the mouth and throat, and disruptions here can contribute to inflammation that travels beyond the mouth into systemic health. The menopause-gut microbiome review notes oral health as one of the systemic areas affected by declining estrogen and reduced microbial diversity.
Estrogen supports skin moisture, elasticity, and the barrier function that keeps harmful bacteria out. As estrogen declines, skin barrier function weakens, altering the microbial environment on the skin's surface. This contributes to skin dryness, increased sensitivity, and slower wound healing, all of which many women notice in perimenopause.
The lungs have their own microbial populations that influence respiratory immunity and inflammation. Systemic inflammatory changes driven by hormone decline can affect the respiratory microbiome, contributing to increased sensitivity to environmental triggers.
The ocular surface has a unique microbial community that protects against infection and maintains moisture. Dry eyes, which are very common in menopause, are partly a microbial issue. Estrogen decline affects the composition of the eye's protective microbial layer.
Why This Matters for How You Support Yourself
If you know that all seven of these microbiome systems are affected by estrogen decline, the logic of supporting your microbiome broadly starts to make a lot more sense.
A probiotic that only addresses gut bacteria is doing partial work during menopause. The symptoms many women experience including recurring UTIs, vaginal dryness, skin changes, oral sensitivity, and persistent digestive issues are all microbiome problems as much as they are hormonal ones. They are connected.
When I discovered that doTERRA PB Restore was formulated specifically to support all of the body's microbiomes and not just the gut, it was the first time a supplement made sense to me in the context of everything I was experiencing. The 24 probiotic strains across 22 species, the dual-chamber delivery system, and the inclusion of pre-, pro-, and postbiotics plus bacteriophages were all designed with whole-body microbiome health in mind.
This does not mean one supplement fixes everything. Dietary fiber, fermented foods, stress management, and sleep all play a role in microbiome health across these systems. But understanding that your symptoms are connected through this shared microbial foundation changed how I approached supporting my body. I stopped chasing individual symptoms and started thinking about the whole system.
If you want to go deeper on what to look for in a probiotic, including why most products fall short, that is covered in what to actually look for in a probiotic. And if you want to understand why fiber is the other half of the microbiome picture, fiber and probiotics in menopause covers that.
Sources & Research
- Liu Y, et al. "Gut microbiota has the potential to improve health of menopausal women by regulating estrogen." Frontiers in Endocrinology. 2025. On the bidirectional relationship between gut microbiota and estrogen, and the large-scale survey showing reduced gut microbiome diversity after menopause. Read study
- Liaquat M, et al. "The gut microbiota in menopause: Is there a role for prebiotic and probiotic solutions?" Women's Health. 2025. Review covering how menopause-associated hormonal changes are linked to decreased gut microbial diversity and reduced Lactobacillus populations, with implications across multiple body systems. Read study
- Barrea L, et al. "Probiotics and prebiotics: any role in menopause-related diseases?" Current Nutrition Reports. 2023;12:83-97. Review on the role of gut microbiota modulation in managing menopause-associated health changes including cardiovascular, bone, and metabolic health. Read study
- Hickey M, et al. "Vaginal microbiome changes during the menopause transition." Research supporting the connection between estrogen decline, Lactobacillus reduction, and vaginal microbiome disruption in perimenopause and post-menopause.
- Sender R, et al. "Revised estimates for the number of human and bacteria cells in the body." Cell. 2016;164(3):337-340. On the equal ratio of microbial cells to human cells and the scale of the body's microbial ecosystem. Read study