gut health menopause microbiome perimenopause women's health Jun 03, 2024

Perimenopause can often feel like a constant battle against your own body, especially when it comes in hot with mood swings, stubborn weight gain, and sleep that is just like a newborns - waking every few hours!

What if I told you that many of these issues might be rooted not just in your ovaries and brain, but in your gut?

More than 2000 years ago Hippocrates told us that all disease begins in the gut, and he sure wasn’t exaggerating when it comes to your hormones! I’m taking you on a deep dive into the intricate world of your gut microbiome and estrobolome, and the role it plays in your perimenopause symptom picture.


What is often simply referred to as 'the gut' is actually a complex system that starts at your mouth and ends at your anus. It includes everything in between: the mouth, esophagus, stomach, small and large intestines, and the supportive organs like the liver, pancreas, and gallbladder.

Each part of your gut has a specific role in breaking down food, absorbing nutrients, and expelling waste.

All of your cells in your intestines have estrogen and progesterone receptors. This is why, through your cycle, but particularly in the few days just before and at the start of your bleed, you may have noticed changes in your bowel motions - becoming more firm or even constipated, before becoming looser during your bleed. You may even notice more bloating in that time frame.

Your female hormones influence how quickly food moves through your gut, how much fluid your body retains, and even how effectively nutrients are absorbed. Such changes can exacerbate or lead to symptoms like bloating, constipation, or diarrhea.

During perimenopause, the impact of your female hormones on your gastrointestinal system (the gut) is still there. However the more frequent fluctuations in hormone levels, especially of estrogen, while progesterone declines, contributes to more of an impact on this system. Many women begin to notice more gut and digestive issues during perimenopause, but might not associate it with hormone fluctuations as such, and keep eliminating foods or adding supplements/remedies in the quest to stop the issues.


Your gut microbiome is made up of trillions of bacteria, fungi, and viruses, each playing a role in your health. These microorganisms help break down food, produce vitamins, and protect against invading pathogens (baddies). They also influence your immune system, weight, and even mood, because of their impact on the production of hormones and neurotransmitters (brain messenger compounds) like serotonin and dopamine in your gut.

Ideally your little microbe friends live in your large intestine only. Sometimes they can make their way into the small intestine, which can lead to trouble and more bloating, reflux, and food sensitivities.

During perimenopause, the balance of these microorganisms can be thrown off by hormonal changes that slow your digestive function and reduce secretions. When we have an imbalance in the microbiome it’s referred to as dysbiosis.

Lots of different factors can influence the mix of bacteria, funghi, and yeasts in your body. Some things to consider:

- Eating a diet high in processed foods or sugar,
- Antibiotics and/or particularly lots of them as a young child,
- Allergies,
- Lack of sleep (isn’t it so interesting what lack of sleep impacts?)
- Alcohol, really irritating to your gut and microbiome,
- Some medications;
- Environmental toxins like chemicals and additives in our food, preservatives,
- How you were born - surgically or vaginally,
- What you ate as an infant, whether you were breastfed, whether you got colostrum,
- Your genetics, and even
- Where you live

One that I am forever talking about is stress.

Whether physical or emotional, stress (specifically your stress response hormone, cortisol), negatively impacts your microbiome and gut health, because it reduces the mucous lining in your intestines that your good bacteria like to live in and feed off. With less mucous lining there is less food for them to grow and thrive in, and less protection for your cells that make the intestinal wall from the baddies (invading pathogens) and other irritants.

It’s also really important to know that if you have experienced some of these factors, and suspect dysbiosis, all is not lost. You can do something about it.


Within your microbiome, there is a collection of bacteria in your gut specifically involved in metabolising estrogens. There are about 60 species that we know of, and together they form your estrobolome. They are crucial because they help maintain healthy estrogen levels in your body, when they are in balance.

Metabolism of estrogen is a multi-step process that involves a collaboration between your liver and estrobolome:

  • Phase 1: Estrogens are processed in the liver and broken down into smaller forms, some of which are lesspotent, while others are more potent or ‘bad’ (in that they can cause DNA damage and lead to the initiation of breast cancer).
  • Phase 2: In the liver these are then conjugated via up to three different processes to other molecules, making them water-soluble and ready to be excreted by the large intestine.
  • Phase 3: The last step in estrogen metabolism is to remove them from the body via your bowel motion (poop!).

Deconjugation by the Estrobolome:

Once in the gut, the estrobolome works to deconjugate estrogen from these molecules through the action of the enzyme beta-glucuronidase, an enzyme produced by the microbes. This allows estrogen to be reabsorbed into the bloodstream where they can act on cells again. Ideally, these conjugated estrogens are passed out of the body, although in menopause when estrogen is low, it is good to have some estrogen reabsorbed.

An imbalance in the estrobolome and thus beta-glucuronidase activity can lead to too much reabsorption, contributing to estrogen excess. Estrogen excess contributes to symptoms like heavy bleeding, PMS, breast tenderness, short cycles.

Conversely, if the estrobolome is smaller than it should be, then there is too little beta-glucuronidase, and less estrogen being recirculated.


Ultimately, we want our estrobolome to be like Goldilocks’ porridge - not too much, not too little, but just right. Especially in perimenopause when estrogen is ping-ponging between high and low, we don’t need our microbiome making the situation worse!

How do you get that balance? I’m glad you asked. Here’s how you can actively support and optimise your gut microbiome:


Incorporating a total of 600g of (non-starchy) vegetables, fruit, herbs, and spices each day is a wonderful way to support your microbiome and gut health. We often think of the benefit of vegetables and fruit, but using herbs and spices like turmeric, ginger, rosemary and garlic can support a healthy gut microbiome too. These foods are rich in antioxidant, anti-microbial, and anti-inflammatory compounds that help reduce gut inflammation and promote a healthy environment for your beneficial bacteria, while keeping the baddies down.


Resistant starches, found in foods like cooked and cooled potatoes, rice or pasta, green bananas, and legumes, feed the good bacteria in your gut. They resist digestion until they reach your colon, where they are fermented by your good microbes to help to produce fuel for themselves and your intestinal cells healthy and reduce inflammation.

Eating your carbs in this way helps reduce their impact on your blood sugar and insulin levels. Its like having your cake and eating it too!


In my opinion, there’s lots of reasons to avoid snacking! We’ve grown up being told it’s best to eat 6 small meals per day. But I’m calling BS to that!

Reducing the frequency of your meals allows time for your self-cleaning mechanism - the migrating motor complex (MMC) to clear out food residue and wastes from your small intestine. The MMC prevents bacterial overgrowth and ensures regular bowel movements. This process is especially crucial in perimenopause, as hormonal fluctuations can slow down your digestive system, leading to bloating and discomfort.


Maintaining regular bowel movements is essential for supporting a healthy microbiome and estrobolome, which in turn helps regulate hormone levels. When you make it a priority to “poop every day,” you aid your body in the elimination of toxins and excess hormones, particularly estrogen.

It’s really important to use your bowels every day, if you’re not, you’re constipated! Incorporating a diet rich in fibre from vegetables, fruits, lentils, beans, and whole grains can naturally promote daily bowel activity. If 600g of veg/fruit doesn’t keep you moving, then I also love adding 2 tablespoons of ground flaxseeds to my breakfast. This has the benefit of a serve of phytoestrogens, anti-inflammatory omega-3 fats, and other vitamins with your fibre.

Managing your gut health is a powerful way to mitigate some of the most challenging symptoms of perimenopause. By understanding the gut-hormone link and taking steps to support your microbiome and estrobolome, you can significantly influence your hormonal balance and overall well-being as you help your body better adjust to the natural hormone changes of perimenopause.

Ready to learn more? Dive deeper into the subject by listening to the full podcast episode below. If you’re looking for more personalised support that tells you what to do and the resources to implement the changes, book a free Clarity Call with me. Together, we can create a plan to suit your body’s needs, your biochemistry, to help reduce symptoms by supporting your body to adapt to the hormone changes of perimenopause.


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