In over twenty years of working with women during perimenopause and beyond, there’s one conversation I find myself having more than any other: “I’m doing everything right, so why do I still feel so off?”
They’re eating well. They’re moving their bodies. They might even be on HRT. But the bloating won’t shift, their energy crashes by mid-afternoon, their mood feels unpredictable, and their periods (if in perimenopause) have taken on a life of their own.
More often than not, the missing piece isn’t what they’re doing. It’s what’s happening inside their gut.
How your gut influences hormone balance
When we think about hormones, we tend to think about our ovaries, our thyroid, maybe our adrenals. We rarely think about our digestive system. But your gut is deeply involved in how your body produces, processes, and eliminates hormones. This is particularly true of oestrogen, which influences everything from your menstrual cycle and your mood to your bones, brain, and cardiovascular health.
Your gut microbiome (the trillions of bacteria living in your digestive tract) doesn’t just digest your food. It communicates with your immune system, produces neurotransmitters like serotonin, manufactures certain B vitamins and vitamin K, and plays a direct role in regulating your hormonal environment. When your microbiome is balanced and diverse, these processes hum along beautifully. When it’s disrupted through stress, poor diet, antibiotics, or the natural hormonal shifts of perimenopause, the ripple effects reach far beyond your digestion.
What is the estrobolome?
The estrobolome is a specific collection of bacteria within your gut microbiome whose role is to metabolise oestrogen. These bacteria produce an enzyme called beta-glucuronidase, which determines how much oestrogen remains active in your body and how much is excreted. When your estrobolome is healthy, it helps maintain the delicate balance of circulating oestrogen that your body depends on.
It’s a term I come back to constantly in my work at The Better Menopause, and it’s something I believe every woman should understand. Once you see how this system works, the connection between gut health and hormonal symptoms suddenly makes complete sense.
How the estrobolome controls your oestrogen levels
Here’s the process in simple terms. After your body has used oestrogen, it’s sent to the liver where it’s packaged up (or “conjugated”) ready for elimination through the gut. Once it arrives in the intestines, the bacteria in your estrobolome decide what happens next.
If your estrobolome is functioning well, the right amount of oestrogen is reactivated by beta-glucuronidase and returned to circulation, while the rest leaves the body as it should.
But if your gut is out of balance, a state known as dysbiosis, this finely tuned process goes wrong. Too much beta-glucuronidase activity can mean excess oestrogen is reabsorbed back into the bloodstream instead of being cleared. This can contribute to what’s often called oestrogen dominance: heavy periods, breast tenderness, PMS, hormonal headaches, and mood swings. Too little activity, on the other hand, means lower circulating oestrogen, which accelerates the symptoms we associate with perimenopause and menopause, including hot flushes, brain fog, joint pain, and low mood.
Put simply, even if your ovaries are producing oestrogen normally, your gut bacteria are having a major say in whether that oestrogen is actually available for your body to use.
How declining oestrogen affects your gut microbiome
What makes this even more compelling is that the relationship between your gut and your hormones runs in both directions.
Oestrogen itself helps maintain the diversity and resilience of the gut microbiome. So as oestrogen levels begin to fluctuate and decline during perimenopause, gut diversity often drops with it. Research has shown that postmenopausal women tend to have a less diverse microbiome than premenopausal women, and that this shift begins during the perimenopausal transition, often years before periods actually stop.
This creates a vicious cycle. Falling oestrogen reduces gut diversity, which weakens the estrobolome, which further reduces active oestrogen, which in turn further disrupts the microbiome. Many of the symptoms women experience during perimenopause (digestive changes, stubborn weight gain around the middle, mood fluctuations, fatigue, brain fog) aren’t simply a result of declining hormones alone. They’re the result of this gut-hormone feedback loop unravelling.
Phytoestrogens and the estrobolome: why what you eat matters even more than you think
The estrobolome doesn’t only process the oestrogen your body produces. It also plays a crucial role in converting plant-based compounds called phytoestrogens into forms your body can actually use.
Phytoestrogens are naturally occurring compounds found in foods like flaxseeds, lentils, chickpeas, soy, and sesame seeds. They’re structurally similar to human oestrogen and can bind to oestrogen receptors in the body, offering a gentle, supportive effect. This is particularly valuable when your own oestrogen levels are declining.
But here’s the key point: your body can only make full use of these dietary phytoestrogens if your estrobolome is healthy enough to convert them. A healthy gut microbiome transforms phytoestrogens into active metabolites like equol and enterolignans, which have been associated with reduced menopausal symptoms and broader protective health benefits. A disrupted gut simply can’t perform this conversion effectively, meaning you could be eating all the right foods and still not getting the full hormonal benefit.
This is one of the reasons I’m so passionate about gut health as a foundation for nutrition during perimenopause. It’s not just about what you eat. It’s about whether your body is equipped to use it.
Signs your estrobolome may need support
So how do you know if your estrobolome might be struggling? There’s no single test for it, but there are patterns I see time and again in the women I work with. If several of the following feel familiar, your gut-hormone axis may well be out of balance:
Persistent bloating or digestive discomfort, especially around your period or during perimenopause. Worsening PMS symptoms, including mood swings, irritability, breast tenderness, or headaches that seem to be intensifying with age. Heavy or irregular periods. Stubborn weight gain, particularly around the midsection. Fatigue and energy crashes that aren’t explained by sleep alone. Brain fog or difficulty concentrating. Increased anxiety or low mood. Hormonal skin changes such as adult acne or dryness. Hot flushes or night sweats that feel disproportionate to your stage of perimenopause.
None of these symptoms exist in isolation. They’re often connected, and the gut is frequently the common thread.
How to support your gut health and hormone balance naturally
The good news is that your microbiome is remarkably responsive to change. Unlike your genetics, your gut bacteria can be meaningfully shifted through what you eat, how you move, and how you live. Here’s where I’d start.
Eat for microbial diversity
The single most powerful thing you can do for your estrobolome is to eat a wide variety of plant-based foods. Aim for thirty different plants across the week: vegetables, fruits, wholegrains, legumes, nuts, seeds, herbs, and spices all count. Each one feeds different strains of bacteria, helping to build the diverse, resilient microbiome your estrobolome depends on. Pay particular attention to phytoestrogen-rich foods like flaxseeds, lentils, chickpeas, and sesame seeds, which give your gut bacteria the raw materials to produce those beneficial oestrogen-like compounds.
Include fermented foods daily
Yoghurt, kefir, sauerkraut, kimchi, miso, kombucha. These foods contain live bacteria that support your existing microbiome. A small portion daily, varied across different types, gives you the broadest benefit. Think of them as reinforcements for the good bacteria already working hard in your gut.
Prioritise fibre
Fibre is the primary fuel for your beneficial gut bacteria. When they ferment it, they produce short-chain fatty acids like butyrate, which support your gut lining, reduce inflammation, and improve insulin sensitivity. All of these matter enormously during the hormonal shifts of perimenopause. Most women in the UK fall well short of the recommended 30g a day. Building up gradually is important to avoid discomfort.
Move your body regularly
Exercise doesn’t just support your muscles, bones, and mental health. It genuinely changes your microbiome for the better. Research shows that regular physical activity increases microbial diversity and promotes the growth of beneficial bacterial species. It doesn’t have to be intense. A Pilates session, a strength workout at home, a yoga flow, a brisk walk: consistency matters far more than intensity. Making movement part of your daily routine is one of the simplest and most effective ways to support both your gut and your hormones at the same time.
Manage your stress
Chronic stress raises cortisol, which directly damages gut lining integrity and reduces microbiome diversity. It also worsens hormonal symptoms, creating yet another feedback loop. Whatever helps you decompress (breathwork, time outdoors, restorative movement, connection with friends), treat it as essential, not optional.
Consider targeted probiotic support
Diet and lifestyle form the foundation, but during perimenopause and menopause the gut sometimes needs more specific help. Not all probiotics are the same, and a general supplement won’t necessarily contain the strains that matter for hormonal health.
This is the reason we developed Better Gut at The Better Menopause. It contains six clinically studied bacterial strains at 50 billion CFU, each selected specifically for its role in supporting the gut-hormone axis during perimenopause and beyond. The strains were chosen not only for their individual benefits (from easing bloating and supporting mood to reducing hot flushes) but because they work synergistically together, helping to restore the kind of microbial balance your estrobolome needs to function properly. You can read more about the specific strains and the research behind them here.
The bottom line: your gut is the foundation of hormone health
Your gut is not separate from your hormones. It’s intimately involved in how your body manages oestrogen, how it responds to stress, how well you absorb nutrients, and how you feel day to day. The estrobolome, that quiet, powerful collection of bacteria determining your oestrogen balance, deserves far more attention than it currently gets.
For women navigating perimenopause and beyond, supporting the microbiome isn’t a wellness trend. It’s one of the most evidence-based things you can do to take back control of how you feel.
The power of great nutrition is available to everyone, and it starts in your kitchen. But sometimes your gut needs a little extra help to catch up, and that’s nothing to feel guilty about. It’s just good science.
ABOUT THE AUTHOR
Joanna Lyall: Founder & Head of Nutrition of The Better Menopause | Nutritional Therapist (Dip Nut, mBANT, CNHC)
Jo embarked on her journey as a certified nutritional therapist in 2006, establishing her own private practice dedicated to enhancing women’s health and optimising hormonal balance. With a wealth of experience spanning over two decades, Jo passionately champions the transformative potential of nutrition, holistic wellness, and complementary health practices.
Frequently asked questions
What is the estrobolome and why does it matter?
The estrobolome is a collection of gut bacteria responsible for metabolising oestrogen. It produces an enzyme called beta-glucuronidase that determines how much oestrogen stays active in your body. When the estrobolome is healthy, it helps maintain balanced oestrogen levels. When it’s disrupted, it can contribute to both oestrogen excess and deficiency, driving symptoms from PMS and heavy periods through to hot flushes and brain fog.
Can probiotics help balance hormones during perimenopause?
Specific strains of probiotics can support the gut environment that your estrobolome needs to function properly. They don’t replace oestrogen directly, but by restoring microbial diversity and supporting gut lining integrity, they can help your body process and regulate hormones more effectively. The key is choosing strains that have been clinically studied for hormonal health rather than a generic formulation.