Your gut is running your hormones. Here’s how.

There is a collection of gut bacteria responsible for metabolising oestrogen, and when it is out of balance, oestrogen clearance goes wrong in a way that directly affects your mood, anxiety, and cognitive function. Most women in perimenopause have never been told this.

Most women focus on their hormones when their mood starts to shift in perimenopause, and far fewer think about their gut. But the two are directly connected and understanding that connection can change how you approach what is happening in your body.

The missing piece nobody mentioned

Perhaps you are in perimenopause and you have already done the right things. You are on HRT, taking supplements for sleep, mood, and energy, eating well. And still your mood and hormones do not feel stable.

Perhaps you know your mood tracks with your hormones, but you cannot get ahead of it. There are good weeks and bad weeks with no clear pattern, and yet your blood tests look normal.

If this is you, there is something worth knowing. Your gut may be directly affecting how your oestrogen behaves in your body. Not in a general dietary sense, but through your gut microbiome specifically. And most women have never been told this.

What is the estrobolome?

Your gut microbiome contains a specific collection of bacteria called the estrobolome, and its job is to help metabolise oestrogen.

Once your body has used oestrogen, whether you are still cycling or using HRT, your liver processes it and packages it for excretion. Oestrogen leaves the body via the kidneys and urine, but also through the digestive system, and this is where the estrobolome handles the final stage of clearance via the bowel.

When the estrobolome is healthy, oestrogen is cleared efficiently. When gut dysbiosis is present and the estrobolome is out of balance, something quite different happens.

What goes wrong: the beta-glucuronidase problem

Beta-glucuronidase is an enzyme produced by both human cells and gut bacteria. Its primary function is to break the chemical bonds that the liver attaches to hormones, toxins, and waste products during detoxification, preparing them for either excretion or reabsorption.

The problem arises when gut bacteria are out of balance. Beta-glucuronidase becomes overactive and breaks apart oestrogen that has already been packaged and sent to the bowel for removal. Instead of leaving the body, that oestrogen gets reabsorbed back into circulation, resulting in excess oestrogen or levels that fluctuate erratically, because your gut is recirculating what should have already been cleared.

How this connects to your mood

Oestrogen is an active regulator of the neurotransmitters that govern mood. It supports serotonin production and receptor sensitivity, influences dopamine (which drives motivation, pleasure, and reward), and modulates noradrenaline, which affects how alert and emotionally responsive you feel. When oestrogen fluctuates erratically because of poor estrobolome function, those neurotransmitter systems become less stable alongside it, which is part of why two women at the same stage of perimenopause, with similar hormone levels on a blood test, can have very different emotional experiences.

There are also two further routes through which gut health affects mood directly, independently of oestrogen.

Approximately 90 percent of serotonin is produced in the gut, not the brain. When gut bacteria are out of balance, that production is directly affected, which means you can have declining oestrogen and compromised serotonin production at the same time, driven by the same root cause.

A compromised gut lining also allows bacterial products to cross into the bloodstream and trigger low-grade inflammation. That inflammation crosses the blood-brain barrier, and neuroinflammation is a recognised driver of low mood, anxiety, and poor stress resilience. It is something we see regularly in clinic here at Urban Wellness.

To summarise, the gut affects mood through at least three routes:

• Oestrogen recirculation

• Serotonin production

• Neuroinflammation

These are not separate problems. They tend to occur together, particularly in perimenopause and menopause.

One important point about gut symptoms

You do not need to have obvious digestive problems for this to be relevant to you. Bloating, constipation, and reflux are signs that something is off, but a compromised estrobolome can be present even when your gut feels entirely normal. This is why many of the women we work with have no obvious gut symptoms at all.

What can negatively affect the estrobolome

• Antibiotics, even a single course, can significantly reduce microbiome diversity

• Ultra-processed food and low fibre intake: gut bacteria feed on fibre, and without varied sources, diversity drops

• Chronic stress, which alters gut motility, reduces microbiome diversity, and increases gut permeability

• Long-term use of NSAIDs, proton pump inhibitors (such as omeprazole or lansoprazole), opiates, and steroids

• A low-variety diet, even an otherwise healthy one: eating the same foods repeatedly narrows the range of bacteria that thrive

What supports a healthy estrobolome

• Diversity of plant foods: aim for 30 different plant foods per week, including vegetables, fruit, herbs, spices, nuts, seeds, and legumes. The range matters as much as the quantity.

• Fermented foods: sauerkraut, kimchi, kefir, and live yoghurt introduce beneficial bacteria directly. Start with small amounts if your digestion is sensitive or these are new to you, as it can take time for your gut microbiome to adjust.

• Prebiotic fibre: onions, garlic, leeks, asparagus, Jerusalem artichoke, and green banana feed the beneficial bacteria already in your gut and are specifically useful for estrobolome support, if tolerated.

• Polyphenol-rich foods: berries, olive oil, dark chocolate (85 percent and above), green tea, and red onions have direct anti-inflammatory effects and act as prebiotics.

• Cruciferous vegetables: broccoli, cauliflower, kale, and Brussels sprouts support both liver oestrogen processing and gut health. Particularly relevant when oestrogen clearance is a concern; aim for two cups a day.

• Probiotic support where needed: Lactobacillus acidophilus and Bifidobacterium longum have the most evidence for supporting healthy beta-glucuronidase activity. There are some good estrobolome-specific products available but food first is always the approach we take in clinic.

What testing can tell you

Functional stool testing can measure beta-glucuronidase activity directly, alongside markers of dysbiosis and intestinal permeability, and it is something we use regularly in clinic. Personalising gut support based on what is actually happening for the individual is far more effective than guessing, and standard GP stool testing does not look at any of these markers.

This is not a prerequisite for starting. The dietary and lifestyle foundations above are worthwhile for almost anyone in perimenopause. But for women with significant or persistent mood or hormone symptoms who have already addressed the obvious factors, functional testing can clarify exactly what is happening and allow us to target support precisely.

If you have done everything right and still do not feel stable

Addressing hormones without looking at gut health often produces partial results, because the two systems are directly connected. If you have optimised your HRT, taken the supplements, and still feel like your mood and energy are at the mercy of something you cannot pin down, your estrobolome is worth investigating.

To understand more about how the gut and brain communicate beyond the oestrogen pathway, take a look at the companion piece on Urban Wellness: What is the gut-brain axis, and why does it matter for your mood in midlife?

If you would like to explore this further with proper testing and a personalised approach, get in touch.