How Gut Bacteria Help Regulate Estrogen

Gut health and hormone health are more connected than many people realize. The bacteria living in your gut do more than help digest food — they also help process hormones, including estrogen. 

Estrogen influences many aspects of health, from mood, metabolism, and bone health to menstrual cycles, perimenopause, menopause, and estrogen-sensitive conditions. More estrogen exposure may contribute to estrogen-sensitive symptoms, including heavy menstrual bleeding, fibroids, and endometriosis. Lower estrogen levels, especially during perimenopause and menopause, are linked with symptoms such as hot flashes, sleep disruption, and bone loss. 

Estrogen metabolism matters because it helps determine not only how much estrogen the body produces, but also how much remains active, how much is recycled, and how much is eliminated.

Clinicians describe the bidirectional relationship between estrogen and the gut, the estrogen–gut microbiome axis. A key part of that axis is the estrobolome, the collection of gut bacterial genes involved in estrogen metabolism. In simple terms, the estrobolome helps determine how much estrogen is eliminated from the body and how much is reactivated and returned to circulation.

Ideally, the body manages the right balance between how much estrogen is biologically “active” and able to influence tissues throughout the body versus how much estrogen is chemically “packaged” and prepared for elimination from the body.

Some “packaged” estrogen, called conjugated estrogen, travels through the intestinal tract on its way out of the body. It is here that gut bacteria can influence what happens next. Various gut bacteria produce the enzyme β-glucuronidase. Enzymes are proteins that help chemical reactions in the body. The β-glucuronidase enzyme can act on conjugated estrogen to remove its chemical “packaging,” converting the estrogen back into its free, biologically active form.

Once reactivated, some estrogen can be reabsorbed through the intestinal lining and returned to circulation through a recycling process known as enterohepatic recirculation. This is one reason the gut microbiome is considered an important regulator of estrogen availability. When the gut microbiome is disrupted — a state known as dysbiosis — estrogen metabolism may also shift, ending in more or less active estrogen circulating through the body. 

SIBO is one example of gut dysbiosis because it involves an abnormal overgrowth of bacteria in the small intestine. While SIBO does not necessarily cause hormone imbalance, it is part of the broader conversation about how changes in gut bacteria may affect systems beyond digestion.

Researchers are still studying exactly how these patterns work. In some cases, higher β-glucuronidase activity may mean more estrogen is reactivated and reabsorbed. In other cases, reduced microbial diversity may impair estrogen recycling, which may be especially relevant during perimenopause and menopause, when estrogen levels are already changing.

For people living with SIBO or IBS-like symptoms, this connection can be an important piece of the puzzle. Hormone changes may affect how the gut feels and functions, while changes in gut bacteria may influence how estrogen is processed and recycled. That does not mean every hormone symptom begins in the gut, but it does mean the gut deserves a place in the conversation.

Key Resources

Baker, J. M., Al-Nakkash, L., & Herbst-Kralovetz, M. M. (2017). Estrogen–gut microbiome axis: Physiological and clinical implications. Maturitas, 103, 45–53. https://doi.org/10.1016/j.maturitas.2017.06.025

Ervin, S. M., Li, H., Lim, L., Roberts, L. R., Liang, X., Mani, S., & Redinbo, M. R. (2019). Gut microbial β-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens. Journal of Biological Chemistry, 294(49), 18586–18599. https://doi.org/10.1074/jbc.RA119.010950

Hu, S., Ding, Q., Zhang, W., Kang, M., Ma, J., & Zhao, L. (2023). Gut microbial beta-glucuronidase: A vital regulator in female estrogen metabolism. Gut Microbes, 15(1), 2236749. https://doi.org/10.1080/19490976.2023.2236749

Park, S.-L., Kim, M.-S., & Kim, T.-H. (2025). Gut microbiome and estrogen. Journal of Menopausal Medicine, 31, 95–101. https://doi.org/10.6118/jmm.24024

Plottel, C. S., & Blaser, M. J. (2011). Microbiome and malignancy. Cell Host & Microbe, 10(4), 324–335. https://doi.org/10.1016/j.chom.2011.10.003