Gut Bacteria's Role in Oestrogen Metabolism

Author: Jessica Lloyd
Senior Vulvovaginal Specialist Naturopath | BHSc(N) | ISSVD, ISSWSH, BSSM, ATMS

Last reviewed: July 3, 2026

Your gut bacteria and oestrogen have much more to do with one another than you might think. Your gut bacteria regulate oestrogen metabolism, by producing enzymes that cause a cascade of reactions.

The key event in the digestive tract is the deconjugation of oestrogen, meaning the splitting apart of bonds, turning oestrogen from its inactive form into its active form.

We need hormones in both states – active and inactive – depending on their task.

Free, deconjugated oestrogen circulates in the bloodstream, distributing it throughout the body to find its target receptors. You can think of this as a lock and key mechanism. Circulating oestrogen is the key, while the lock, the receptor, remains fixed in tissue. An excellent example of where oestrogen receptors are aplenty is in the vagina.

Without deconjugating – breaking apart – oestrogen properly, we can have far less oestrogen circulating than is optimal. Low levels of circulating, deconjugated oestrogen can lead to low oestrogen symptoms, such as a dry, easily irritated vagina (atrophic vaginitis).

The process of gut bacteria turning oestrogen into a usable form is called the oestrobolome.

Why your bones need oestrogen

Oestrogen slows down a group of cells called osteoclasts, which break down bone. Some bone must be taken away and replaced, but if you don’t have enough oestrogen, osteoclasts are more active, thus breaking down bone at a faster rate than it is replaced.

This bone-robbing process results in low bone density and strength.

The oral contraceptive pill is an example of a drug that results in a loss of bone at a faster rate than you would normally.

Some studies have found that a few different strains of probiotic bacteria, in certain circumstances, can increase bone formation, decrease bone reabsorption, and change the microstructure of bones. These studies were performed on Bifidobacterium longum, Lactobacillus helveticus, and L. reuteri.

Another study into breast health found that women who had a cancer-positive biopsy had far less diversity in their microbiome than the control group.

The study found that circulating oestrogen levels were not related to the microbiome’s composition, which led researchers to believe that the microbiome works independently of oestrogen, but not vice versa.

For a closer look at how this two-way relationship may feed into hormone-driven cancers, see your gut bacteria as an endocrine partner in oestrogen-driven cancers.