Some of your gut bacteria help decide how much oestrogen circulates in your body, and when oestrogen falls at the menopause, the gut changes too. HRT tops oestrogen back up, and the first small studies suggest the gut bacteria of women taking it sit closer to the premenopausal pattern, although this research is young and nothing is settled. The medicine itself can also unsettle digestion at first, with nausea and looser stools the most familiar effects, and these usually fade within a few weeks. This guide covers how oestrogen and gut bacteria affect each other, what changes at the menopause, what is known about HRT and the gut microbiome, and when to see a GP. None of it is a reason to start, stop or change HRT, which is a decision for you and your GP or menopause specialist.
How are oestrogen and your gut bacteria connected?
Oestrogen does not simply do its job and leave the body. The liver packages used oestrogen into an inactive form and sends it into the gut for disposal. Some gut bacteria make an enzyme called beta-glucuronidase, which unwraps that package and releases active oestrogen again, and a portion of it is absorbed back into the bloodstream instead of leaving the body. In effect, these bacteria recycle oestrogen. A 2017 review in the journal Maturitas describes this loop and links it to conditions in which oestrogen levels matter.
Researchers call the full collection of gut bacterial genes that can process oestrogen the estrobolome. The term was coined in 2011 and the idea has held up as the field has grown.
There is human evidence behind it. In a study of 51 adults, men and postmenopausal women with a richer, more varied mix of gut bacteria had higher oestrogen levels in their urine. This was a small group examined at one point in time. It shows a link, not a cause, and it needs repeating in larger groups. The pattern did not appear in premenopausal women, whose ovaries produce so much oestrogen that any contribution from the gut is hard to see.
Once the ovaries wind down at the menopause, the oestrogen the gut recycles becomes a larger share of what remains. That is why researchers studying the menopause have become interested in gut bacteria.
What happens to your gut bacteria at the menopause?
The largest study so far analysed stool samples from around 2,300 adults in the United States, including more than 1,000 postmenopausal women. It found that the gut bacteria of postmenopausal women looked slightly more like men's than like those of premenopausal women, with a tendency towards lower variety and less of the bacterial oestrogen-processing activity described above. The researchers adjusted for age, which is the obvious alternative explanation. Even so, this is an observational study. It cannot prove that the menopause caused the differences, and the women studied were from one population, so the finding may not transfer everywhere.
The evidence here is mixed. A 2026 pooled analysis of seven studies compared women with low oestrogen levels against premenopausal women and found no consistent differences in the variety of gut bacteria or in the major bacterial groups. The included studies measured different things in different ways, and their results varied widely. Menopause probably influences the gut microbiome, but the size and shape of that influence is not yet pinned down.
If you have noticed bloating after eating, wind or a change in bowel habit through perimenopause, hormones are one influence among several, alongside diet, stress and age. If you have IBS, this stage of life can change how it behaves, and our guide to IBS in women covers the menstrual cycle, the menopause and what helps in detail.
Does HRT change the gut microbiome?
HRT replaces the oestrogen the ovaries no longer make, usually alongside a progestogen for women who have a womb. Because oestrogen and gut bacteria influence each other, researchers have asked whether topping oestrogen back up moves the gut microbiome back towards its premenopausal state. A 2023 review concluded that work on this has barely begun, and only a handful of small studies exist.
The most direct study to date is small. Researchers sampled bacteria from the small intestine of 35 women and found that those taking hormone therapy had a bacterial mix closer to that of premenopausal women than women who were not taking it. Thirty-five people is a very small group. The study looked at one point in time, and it sampled the small intestine rather than the stool most microbiome research uses. Early research like this raises a possibility. It does not establish an effect, and no one should take or avoid HRT because of it.
One practical point sits behind this research. Only HRT tablets pass through the digestive system. Patches, gels and sprays deliver oestrogen through the skin, and the NHS guide to the types of HRT explains how the forms differ. Whether the route into the body changes what happens in the gut microbiome has not been properly compared, so there is no evidence-based reason to prefer one form for your gut. The right form of HRT is the one that controls your symptoms and suits your health history, which is a prescribing decision for your GP.
HRT is not in the same category as an antibiotic, which wipes out large numbers of gut bacteria within days. We cover how antibiotics change the gut microbiome separately. Whatever HRT does to gut bacteria appears slower and far subtler, and on current evidence it remains unproven.
What gut side effects can HRT cause?
The NHS lists feeling sick and diarrhoea among the side effects of both oestrogen and progestogen, the two hormones most HRT contains. Many women get no side effects at all, and mild ones usually improve over the first few weeks as the body adjusts. The NHS advice is to give a new HRT prescription around three months if you can, because early side effects commonly settle in that time while the benefit builds.
Side effects of HRT can also look like menopause symptoms, so an unsettled stomach in the first weeks is not automatically the medicine's doing. If gut symptoms are severe, or they are still with you after three months, see your GP rather than putting up with them. There are usually options within treatment, such as a change of dose, a different type of HRT, or a switch from tablets to patches, and finding the right combination often takes a few adjustments. Do not stop HRT on your own without speaking to your GP first, because your menopause symptoms are likely to return and there may be a simpler fix.
Can a gut microbiome test tell you anything useful?
Not about your hormones. A stool test cannot measure oestrogen, cannot tell you whether you are perimenopausal, and cannot tell you whether HRT is working or whether it is right for you. Those questions belong to you, your symptoms and your GP.
A stool test shows which bacteria were present, and in what amounts, on the day you took the sample. That includes overall bacterial variety, and the groups of bacteria researchers are studying for their role in recycling oestrogen. If your digestion has changed through the menopause and you want to see where your gut bacteria currently sit, an at-home gut microbiome test measures which bacteria you carry from a single sample collected at home. A result is context for a conversation with your GP or pharmacist, not a hormone reading. It cannot say whether those bacteria are actively supporting your hormones, what caused the pattern it finds, whether menopause, medicine or diet, and no result from it diagnoses a condition. How to read a result, and where its limits sit, is explained on our page about gut microbiome testing for gut dysbiosis.
How can you look after your gut through the menopause?
If you take HRT, keep taking it exactly as prescribed, and take any problem to your GP or pharmacist rather than adjusting anything yourself. With that in place, a few things support the gut side.
- Eat a wide range of plants. Gut bacteria live on plant fibre, and variety in what you eat supports variety in what you carry. UK guidance is around 30g of fibre a day, and most of us eat much less, so increase it gradually to keep bloating manageable
- Include fermented foods if you enjoy them. Live yoghurt, kefir, sauerkraut and kimchi all bring live cultures with them
- Keep moving. Regular activity supports regular bowels, and it is one of the few habits with benefits for menopause symptoms and digestion at the same time
- Speak to a pharmacist before adding herbal menopause remedies. Products such as black cohosh and St John's wort are not tested the way medicines are, and some interact with prescription medicines. The NHS page on alternatives to HRT covers this in more detail
Nothing on this list treats menopause symptoms, and none of it replaces HRT or any other prescribed treatment. For more on eating for your gut bacteria, the best foods for gut health guide goes into detail.
When should you see a GP?
Two sets of warning signs need a GP appointment rather than a routine review.
The first is bleeding. Irregular vaginal bleeding or spotting is common in the first few months of HRT and usually settles. See your GP if irregular bleeding carries on for more than six months after starting HRT, if it becomes heavier, or if you bleed after your periods have stopped for a while. Bleeding after the menopause always needs checking, whether or not you take HRT.
The second is the gut itself. Book a GP appointment for blood in your stool or black, tarry stools, a change in bowel habit lasting more than three weeks, unexplained weight loss, difficulty swallowing, persistent vomiting, or gut symptoms that begin for the first time over the age of 50 or alongside a family history of bowel or ovarian cancer. Persistent bloating is treated differently from bloating that comes and goes. Bloating that is there most days for three weeks or more is one of the symptoms the NHS asks women to have checked, particularly with pelvic pain, feeling full quickly or needing to wee more often. It usually has an ordinary explanation, and getting it looked at is how you find that out.
Gut side effects from HRT that are milder than any of this but not settling are still worth an appointment, because dose and type changes exist precisely for that situation. If your menopause symptoms are proving hard to manage, you can also ask your GP whether a referral to an NHS menopause specialist is available in your area.
This guide is for information only and does not replace medical advice. Speak to your GP or pharmacist about your own treatment.
Sources
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- Peters BA, Lin J, Qi Q, et al. (2022). Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Cardiometabolic Risk in the Hispanic Community Health Study/Study of Latinos. mSystems. PubMed | DOI
- Saravinovska K, Santi D, Costantino F, et al. (2026). The impact of estrogen status on the gut microbiome: a systematic review and meta-analysis. Frontiers in Endocrinology. PubMed | DOI
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- NHS. Types of hormone replacement therapy (HRT). nhs.uk
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