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How Digestive Health and the Microbiome Influence Hormone Balance

a woman drinking tea for digestive and hormonal health

Optimal digestive function is important for so many aspects of our wellbeing especially estrogen and progesterone balance. The liver, gallbladder and intestines play an important role in managing the circulation and excretion of these hormones and if metabolism isn't working well you can experience PMS, irregular periods, acne, thyroid disease and autoimmune disease.

In this post I want to talk about the topic of gut health and hormone balance. I'll also discuss ways to improve symptoms of hormone imbalance such as PMS, painful periods, cramping, and acne with dietary changes, fiber, probiotics and weight management.

How is gut bacteria related to estrogen?

There are different forms of estrogen including estrone (E1), estradiol (E2) and estriol (E3). E1 is a weak form of estrogen present in post-menopausal women. E2 is a potent and active form of estrogen and is predominant in premenopausal women. It's involved in regulating the menstrual cycle. E3 is a less potent form of estrogen that is mostly present in pregnant women and produced by the placenta.

Estrogen is involved in more than reproductive health, it plays an important role in cardiovascular health, atherosclerosis, cholesterol management, weight, strong bones, and brain function. Before menopause, estrogen is produced by a woman's ovaries, adrenal glands and fat tissue. After menopause, estrogen is produced in the adrenals and fat tissue.

In a previous post I talked about the microbiome, the collection of beneficial bacteria in our digestive systems that are involved in gut health, mood, weight management, nutrient production and immune health, but there's a part of the gut microbiome that is specific to estrogen metabolism called the estrobolome. The bacteria that make up the estrobolome can convert estrogen into an active hormone using an enzyme that releases it from a sugar molecule so it's able to bind to estrogen receptors.

After estrogen is produced it cycles through the digestive system. Some of it becomes attached to bile acids in the liver that aid the breakdown of fat and are eliminated in the stool. However, if bacteria in the gut activate it with enzymes, it can be reabsorbed by the body and lead to excess estrogen circulation. This effect is more likely to happen if there is low bacterial diversity in the gut or dysbiosis.

How do you know if your microbiome or hormones are imbalanced?

Signs of dysbiosis or an imbalance in the digestive system can include gas, bloating, diarrhea, and constipation. Autoimmune disease, allergies, skin issues and digestive diseases can also be related to imbalance.

Signs that estrogen, progesterone and testosterone are out of balance include painful periods, PMS, cramping, irregular periods, heavy periods, mood swings, headaches, and acne.

What can you do to keep your hormones and gut healthy?

  • Use antibiotics only when necessary - antibiotics can be useful in cases where someone is very sick, but they've been overused in the past for conditions where they aren't even effective. Now that we know more about the importance of the microbiome, it's important to use them only when needed to prevent killing off the beneficial bacteria and creating resistant bacterial strains. If you have to take one I recommend taking a probiotic as well and getting plenty of probiotic-rich foods in your diet.

  • Eating phytoestrogens in the diet - these compounds are found in soy, flax seeds, almonds, oats, legumes, lentils, and sesame seeds. Herbal phytoestrogens include red clover and alfalfa. Phytoestrogens resemble estradiol (E2) and can bind to some estrogen receptors. When they bind they promote weak estrogenic activity while also preventing our own stronger estrogen from binding. This can reduce excess estrogen activity.

  • Reduce exposure to xenoestrogens - these are considered "hormone disruptors" that come from plastics, pesticides, cosmetics, and food containers. "Xeno" means "foreign" and these molecules resemble estrogen so closely that they can bind to and stimulate our estrogen receptors. Ways to avoid them include reducing plastic use, not heating or storing food in plastic containers, eating organic produce as much as possible, and switching to natural cleaning and beauty products. For more information check out the Environmental Working Group here.

  • Eat more fiber - eating soluble and insoluble fiber provides the necessary fuel for the gut bacteria and promotes diversity. Good sources include whole grains like brown rice, wheat, oats, and quinoa, seeds like chia and flax and legumes. A diet high in whole fruits and vegetables is also a good idea. Your microbiome changes quickly, within days, once you alter your diet. The fiber will also help your body eliminate excess estrogen through regular bowel movements.

  • Eat fermented foods, prebiotics and probiotics - prebiotics help to feed the good bacteria. Good sources are artichokes, asparagus, bananas, eggplant, garlic, honey, jicama, leeks, legumes, onions and peas. Probiotics are foods that contain the beneficial bacteria themselves. Good sources of these are fermented foods like yogurt, kefir, sour cream, kimchi, kombucha, and miso.

  • Maintain a healthy weight - it was once thought that body fat was inert and didn't really do much, but science is learning more and more about how fat is an active part of our overall health. Hormones are made from fat that control hunger, artery health, energy metabolism, and inflammation. Maintaining a healthy amount of body fat can reduce excess estrogen production.


Healthy digestive function is so important to balanced hormone metabolism, especially estrogen. There are different forms of estrogen including estrone (E1), estradiol (E2) and estriol (E3). Estrogen is involved in reproductive health, cardiovascular health, atherosclerosis, cholesterol management, weight, strong bones, and brain function. There is a part of our microbiome called the estrobolome that regulates estrogen production and circulation. Having good digestive health can help control excess estrogen in the body, reducing symptoms like painful periods, PMS, cramping, irregular periods, heavy periods, mood swings, headaches, and acne. Ways to do this include using antibiotics only when necessary, eating phytoestrogens in the diet, reducing exposure to xenoestrogens, eating more fiber, eating fermented foods and probiotics and maintaining a healthy weight.

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In Health,

Dr. Jamie

This website is not intended for the purpose of providing medical advice. All information, content, and material of this website is for informational purposes only and are not intended to serve as a substitute for the consultation, diagnosis, and/or medical treatment of a qualified physician or healthcare provider.


Baker, James M, et al. “Estrogen-Gut Microbiome Axis: Physiological and Clinical Implications.” Maturitas, U.S. National Library of Medicine, Sept. 2017,

Rietjens, Ivonne M C M, et al. “The Potential Health Effects of Dietary Phytoestrogens.” British Journal of Pharmacology, John Wiley and Sons Inc., June 2017,


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