The Estrogen-Gut Microbiome Axis: Impact on Digestive Health
Article

The Estrogen-Gut Microbiome Axis: Impact on Digestive Health

Published on Monday, June 10, 2024
by
Kitty Broihier

Acid Reflux
GERD
Gut Health

Estrogen impacts your inner ecosystem in ways you might not realize

Your gut health depends on much more than the food you eat. In fact, when it comes to your gastrointestinal function, hormones play a significant role. The gastrointestinal (GI) tract can be considered an endocrine organ since it releases various hormones to influence everything from appetite to digestion, nutrient absorption, and more. For people with ovaries or who take supplemental estrogen, the idea that estrogen, which is not a digestive hormone, and gut health are connected can be surprising news.    

What’s The Estrogen-Gut Microbiome Axis?

Think of the estrogen-gut microbiome axis as a two-way street that allows your gut microbiome to impact your estrogen levels, and your estrogen levels to impact your gut microbiome.

Let me backup a bit and explain how this works. 

Your digestive system is home to a vast community of bacteria, collectively known as the gut microbiome. A growing body of evidence points to the gut microbiome's far-reaching and varied health impacts. For example, the bacteria of the digestive tract have metabolic roles in the body and also impact our risk for chronic diseases like cardiovascular disease, type 2 diabetes, certain cancers, and inflammatory bowel disease. Another job of the gut bacteria is to help regulate the amount of circulating estrogen in people with ovaries. How does this work? The gut bacteria release an enzyme that essentially activates estrogen, allowing it to move through the body and do its work. 

However, when diversity in gut bacteria is compromised (dysbiosis), this process malfunctions, which may contribute to developing conditions like metabolic syndrome, endometriosis, polycystic ovary syndrome, cancer, and other harmful conditions. On the flip side, for people with ovaries or who use supplemental estrogen, the fluctuations of estrogen levels throughout the lifespan can bring changes to the gut microbiome. In other words, the estrogen-gut microbiome axis allows changes on one end of the axis to bring about changes on the other end. And when you add in the natural changes that occur in these systems as we grow, mature and age, you’ve got yourself a fairly complicated relationship. 

Understanding the Gut Impact of Period Fluctuations and Birth Control

Many women report gastrointestinal (GI) issues such as diarrhea, constipation, and bloating at different points during their menstrual cycles. Given the presence of sex hormone receptors along the GI tract, this makes sense. Some studies suggest that changes in estrogen levels during the menstrual cycle impact gut motility and other bowel and gut symptoms. So, does the gut microbiome play a part here? Given the estrogen-gut microbiome axis, it’s plausible that the gut microbiome tempers the impact of estrogen (and progesterone) on the GI tract. 

Taking hormonal birth control, especially the pill form, may mess with your digestive health. A study published in the journal Gut found that, in women with a family history of Crohn’s disease, those who took the pill for at least five years were three times more likely to get the disease than those who didn’t use the pill. Even without a family history of digestive issues, hormonal birth control may lead to symptoms that are common in irritable bowel syndrome (IBS), including bloating, diarrhea, and constipation, which can make it difficult to diagnose the actual cause of the discomfort. 

Menopause Matters for Gut Health

The average woman enters menopause in her early 50s. Put another way, roughly one-third of a woman’s life happens after menopause. Throughout the menopausal transition (perimenopause, menopause, and postmenopause stages), a woman’s body goes through significant changes—some impacting the gut microbiome and overall digestive system function. The gut microbiome balance before menopause is different than after menopause.

When enough estrogen is present, a woman’s gut microbiome contains a healthy balance of bacteria. With menopause, estrogen levels decrease, as does the gut microbiome diversity. It’s speculated that the estrogen-gut microbiome relationship mediates menopausal and postmenopausal weight gain in women. Of course, we don’t know the optimal gut microbial species composition for either gender. Still, it’s becoming clear that populations of pro-inflammatory and obesogenic microbiome species increase in post-menopausal women. 

Estrogen's Role in GERD Symptoms: Exploring Gender Differences and Treatment Implications

Estrogen’s effect on digestive health isn’t limited to the gut microbiome. The presence of estrogen may partially explain gender differences in GERD symptoms. Estrogen increases nitric oxide synthesis, which decreases muscle tone in the lower esophageal sphincter, making acid reflux more likely. With menopause, this effect can be expected to diminish due to a lack of estrogen. And for women who use hormone replacement therapy (HRT), the extra estrogen may stimulate more acid reflux symptoms. But, there may be a silver lining: the anti-inflammatory effects of estrogen tend to decrease the risk of esophageal and GI cancers.

Speaking Up: Why Discussing Gut Health with Your Physician Matters

If your gut health seems “off,” it’s always a good idea to discuss it with your physician. Talking about these issues might feel embarrassing to you, but your doctor has heard it all and considers these topics routine. Estrogen isn’t always at the root of GI discomfort but can be an important contributing factor throughout the life cycle.


  1. Baker, J., Al-Nakkash, L., & Herbst-Kralovetz, M. (2017). Estrogen-gut microbiome axis: Physiological and clinical implications. Maturitas, 103, 45–53. https://doi.org/10.1016/j.maturitas.2017.06.025
  2. Bany, R., Reimann, F. & Gribble, F. (2023). The intestine as an endocrine organ and the role of gut hormones in metabolic regulation. Nat Rev Gastroenterol Hepatol 20, 784–796 (2023). https://doi.org/10.1038/s41575-023-00830-y
  3. Bermingham, K., Linenberg, I., Hall, W., Kade, K., Franks, P., Davies, R., et al. (2022). Menopause is associated with postprandial metabolism, metabolic health and lifestyle: The ZOE PREDICT Study, 85. https://doi.org/10.1016/j.ebiom.2022.104303
  4. Chen, C., Gong, X., Yang, X., Shang, X., Du, Q., Liao, Q., Xie, R., Chen, Y., & Xu, J. (2019). The roles of estrogen and estrogen receptors in gastrointestinal disease. Oncology Letters, 18(6), 5673–5680. https://doi.org/10.3892/ol.2019.10983
  5. Hills, R., Jr, Pontefract, B., Mishcon, H., Black, C., Sutton, S., & Theberge, C. (2019). Gut Microbiome: Profound Implications for Diet and Disease. Nutrients, 11(7), 1613. https://doi.org/10.3390/nu11071613
  6. Khalili H, Higuchi LM, Ananthakrishnan AN, et al. (2013). Oral contraceptives, reproductive factors and risk of inflammatory bowel disease. Gut, 62:1153-1159. https://doi.org/10.1136/gutjnl-2012-302362
  7. Siddiqui, R., Makhlouf, Z., Alharbi, A., Alfahemi, H., Khan, N.. The gut microbiome and female health. Biology. (2022). 11(11):1683. https://doi.org/10.3390/biology11111683
  8. Singh, V., Park, Y., Lee, G., Unno, T., & Shin, J. (2023). Dietary regulations for microbiota dysbiosis among post-menopausal women with type 2 diabetes. Critical Reviews in Food Science and Nutrition, 63(29), 9961-9976. https://doi.org/10.1080/10408398.2022.2076651 

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