How your gut bacteria affect oestrogen levels

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

Last reviewed: July 30, 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.¹

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 Depo-Provera (DMPA) contraceptive injection — not the combined pill — is the contraceptive linked to bone-density loss, because it lowers oestrogen; this loss is largely reversible after stopping. Combined pills are broadly bone-neutral in adults, though very low-dose pills may slightly blunt peak bone-mass building in teenagers.²

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. ^3,4,5

Another study into breast health found that postmenopausal women with breast cancer had significantly less diversity in their gut microbiome than the control group.⁶

The lower diversity in the women with cancer was independent of their oestrogen levels. Interestingly, in the healthy control group, higher total oestrogens were actually associated with greater microbiome diversity — a reminder that the gut and oestrogen influence each other in both directions.

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.

Frequently asked questions

What is the estrobolome?

It is the collection of gut bacteria that process oestrogen. They make an enzyme (β-glucuronidase) that reactivates oestrogen the liver had packaged up for removal, letting it be reabsorbed and circulate again.¹

Can gut bacteria affect my oestrogen levels?

Yes. If this bacterial step is sluggish — for example with low microbiome diversity — less active oestrogen is recycled back into circulation, which can contribute to low-oestrogen symptoms such as a dry, easily irritated vagina.¹

Does the pill cause bone loss?

The combined pill is broadly bone-neutral in adults. It is the Depo-Provera (DMPA) injection that is linked to bone-density loss, and that loss is largely reversible after stopping.²

This article is general information and not a substitute for personalised medical advice. If you have symptoms of low oestrogen or gut issues, please see an experienced practitioner.