Does Menopause Affect Your Gut Microbiome? What the Research Shows

Heard of the gut microbiome? It’s the community of trillions of bacteria, viruses, fungi, and other microbes living in your gut. The microbiome is crucial to your health. When it's disrupted, it doesn’t just affect your digestion; it can affect everything from your mood to your skin.

When this topic comes up, people talk about diet, exercise, alcohol, and even artificial sweeteners. Each of these factors can alter your gut microbiome. But there’s one factor that gets forgotten: menopause.

Women often blame their menopause symptoms on their hormonal changes. And yet, the latest evidence suggests that your gut bacteria might play a surprising role in menopause, offering the potential for new and effective treatments.

Gut Microbiome and Menopause: What's the Link?

Your gut microbiome and the rest of your body constantly exchange signals. What affects one naturally impacts the other.

A big part of this two-way communication is hormones.

During menopause, your reproductive hormones, like oestrogen and progesterone, begin to fall. This can be slow at first, or quite dramatic. But it has big implications for your gut microbiome.

Inside your gut, there’s a group of gut bacteria that process and recycle oestrogen. They’re known as the “estrobolome.” These bacteria determine how much oestrogen is recycled versus excreted from the body. That means any changes in these bacteria can influence menopausal symptoms.

The consequences are wide-reaching. Lower oestrogen levels can affect bone density, metabolic health, cholesterol levels, and cardiovascular disease.

How Your Gut Microbiome Changes Over Time

Menopause is one potential factor causing shifts in your gut microbiome. But it’s not the only one.

From the moment you’re born, your gut microbiome is changing. The first big shift comes when you switch from breast milk to food. Gradually, you then accumulate different species throughout childhood.

The next stage, especially for women, is during puberty. The production of sex hormones increases gut microbiome diversity in females more than in males. After menopause, however, a women’s gut microbiome tends to resemble that of a male’s more than her own pre-menopausal profile.

There are natural fluctuations over your lifetime as well. Antibiotics, processed foods, healthy periods, and more can all influence your gut bacteria, subtly shifting the composition.

Hormones, Menopause, and Gut Bacteria

Your ovaries secrete natural oestrogens throughout your life. You might get a little extra from the contraceptive pill if you take this too. These are filtered from your blood by the liver, which then get excreted in bile.

The same is true for progesterone.

In your gut, the estrobolome helps “recycle” oestrogens. It does this by unbinding the compounds your liver used to metabolise them, allowing them to re-enter your blood supply.

But there’s one part not mentioned. Gut bacteria rely on the flow of oestrogens in the first place. When this starts to decline, the estrobolome becomes less active. With fewer oestrogens circulating, the recycling process weakens, so even less oestrogen is returned to the bloodstream.

It does mean that gut bacteria play a disproportionate role in your oestrogen levels as natural hormone production declines. So, if you can support these bacteria in other ways, it can help soften menopausal symptoms.

The Downsides of Changing Your Gut Microbiome

When falling oestrogen levels combine with shifts in gut bacteria, the effects can ripple far beyond digestion. Some of the most common consequences include:

• More digestive discomfort. Changes in bacterial balance can lead to bloating, constipation, diarrhoea, or food sensitivities that seem to appear out of nowhere.

• Worsening metabolic health. A disrupted microbiome has been linked to weight gain, insulin resistance, and a higher risk of type 2 diabetes, all of which become more common after menopause.

• Bone and heart health. Lower oestrogen levels are closely related to declining bone mass and higher cholesterol levels. This increases the risk of osteoporosis and cardiovascular disease.

• Mood, skin, and inflammation changes. Women commonly notice low mood, joint aches, or skin flare-ups during menopause. But these symptoms are also linked to gut dysbiosis.

How to Support Your Gut Microbiome During Menopause

Menopause is one of the best times to support your microbiome. Here’s what you can do:

• Eat lots of fibre. Fruits, vegetables, legumes, and whole grains fuel your gut microbiome. Choosing a diet rich in different plant species supports microbial diversity.

• Include fermented foods. Foods like yoghurt, kefir, kimchi, and sauerkraut contain helpful microbes that can help recolonise your gut.

• Protect sleep and lower stress. Hormone changes can cause sleep issues or rising stress. Try to counteract these symptoms to safeguard your microbiome.

• Consider HRT. It’s not yet clear whether HRT reverses microbiome changes, but early research suggests it may influence gut composition.

Most of all, get your gut microbiome tested. The Functional Gut Clinic offers personalised microbiome testing for women experiencing menopause. You’ll receive personalised recommendations and dietary guidance to help support your gut.

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