Microbiota and hormonal health: a key connection in women's health

For years we have spoken about hormonal health as if hormones worked in isolation. Today we know the body works as a network of systems in constant communication.

One of the links attracting the most scientific interest is the one between the gut microbiota, oestrogen metabolism and female hormonal health.

This connection becomes especially relevant during stages such as perimenopause and menopause, when hormonal changes may coincide with shifts in different microbial communities.

What is the gut microbiota?

The gut microbiota is the set of microorganisms living in our digestive tract. It is mainly made up of bacteria, although it also includes other microorganisms.

Its composition is unique to each person and is influenced by many factors: diet, age, physical activity, medication, lifestyle, environment and hormonal status.

So when we talk about microbiota, it is not simply a matter of identifying “good” or “bad” bacteria. What matters is understanding the ecosystem as a whole and how it interacts with the body.

Microbiota and hormones: a two-way relationship

The relationship seems to work in both directions. Hormonal changes can modify the environment in which microorganisms live, while certain gut bacteria take part in the metabolism of sex hormones, especially oestrogens.

One of the most studied concepts in this field is the estrobolome: the set of gut bacterial genes related to oestrogen metabolism.

Some bacteria produce enzymes such as β-glucuronidases, able to modify the conjugated oestrogens that reach the intestine. This may influence their reactivation and the enterohepatic circulation of oestrogens.

Put simply: part of the oestrogens the body has already processed can re-enter circulation after interacting with the gut microbiota.

What happens during menopause?

Menopause involves a major endocrine change, particularly the decline in ovarian oestrogens. These hormonal changes can influence different microbial communities, including gut, vaginal and oral ones. At the same time, the microbiota may take part in sex hormone metabolism.

However, it is important to avoid oversimplified conclusions. Current research has not identified a single ideal gut microbiota composition that could be defined as “the microbiota of a healthy woman during menopause”. A systematic review and meta-analysis published in 2026 found no consistent differences in microbial diversity or in the main bacterial groups between women with low oestrogen levels and premenopausal women, and studies show high heterogeneity.

This means we are still learning how this relationship works.

The role of nutrition

Diet is one of the factors that most influences the gut ecosystem. A varied diet including vegetables, fruit, pulses, nuts, seeds and whole grains provides fibre and different compounds that can be used by gut microorganisms.

In addition, some phytoestrogens present in plant foods can be transformed by certain gut bacteria into metabolites such as equol. The ability to produce these compounds is not the same in everyone, as it depends, among other factors, on the presence of specific bacteria.

So rather than looking for a single food or supplement that “balances hormones”, it makes sense to build a varied diet adapted to individual needs.

What about probiotics?

Probiotics, prebiotics and other strategies aimed at modifying the microbiota are being studied as possible complementary tools for health during menopause.

But the evidence is still limited and does not allow us to recommend a specific probiotic as a universal solution for menopausal symptoms. Higher quality clinical studies are needed to determine which interventions may be genuinely useful, for whom and in what circumstances. Personalisation will probably be one of the keys of the future.

How can we look after our microbiota?

There is no single formula, but we can adopt habits that support good gut health: prioritise a varied, plant-rich diet; increase the diversity of fibre sources according to individual tolerance; include fruit, vegetables and pulses regularly; keep physically active; sleep and rest well; avoid unnecessary use of antibiotics and other medication; pay attention to persistent digestive symptoms, and consult health professionals when there are hormonal changes or symptoms affecting quality of life.

Above all, remember that caring for the microbiota does not replace a medical assessment when there is a health problem.

An integrative view of female hormonal health

The connection between microbiota and hormones reminds us of something fundamental: the body does not work in separate compartments. Gut, metabolism, immune system, brain and endocrine system are in constant communication.

During a woman's hormonal transition, understanding these connections can help us develop a more complete view of prevention and health care.

At SHOMMA we are committed to an integrative view of women's health, evidence-based and adapted to each stage of life. Because caring for hormonal health is not only about measuring hormones. It is also about understanding how the whole system works.