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The Secret Relationship You Should Know About: Your Gut and Hormones

At first glance, your gut health and hormone health might not seem related, but there are actually endless connections between the two. As Dr. Ben Schuff, director of Naturopathy and Nutrition at BIÂN Chicago, puts it, “The gut microbiome is the root of our physiologic tree.” He explains that when this root is damaged, the rest of the branches can be disrupted. Hormones are a delicate part of that biological balance.

The relationship between your microbiome and hormones is a two-way street. “Our gut is predominantly made up of what’s called the microbiome, the biodiversity of various bacteria, fungi, and viruses that coexist with us,” Dr. Schuff explains. That microbiome plays an important role in regulating and processing certain hormones like estrogen. In turn, hormones act both generally and locally in our gut to influence its function and overall balance.

As Dr. Schuff says, “Our gut-microbiome is an intelligent system that senses, then influences nearly every hormonal feedback loop in our body.”

First Things First: The Hormone-Gut Connection Also Affects Your Skin

Imbalances in gut hormones can do more than just affect your internal health. They can also be reflected on the surface of your skin. “I always say that the way your body looks on the outside is a direct reflection of what’s going on the inside,” says Dr. Pedre. “In the case of skin conditions, what’s going on inside is almost always an undiagnosed gut health issue that is showing up as inflammation, congestion, or an allergic reaction on the skin.”

Gut and skin health are intimately linked. In fact, Dr. Pedre would go as far as to say that at least 75 percent of his patients with gut health issues also have a skin health issue.

He explains that hormone-disrupting chemicals like BPA increase inflammation, leading to an increased risk for leaky gut and autoimmune disease. Leaky Gut, he says, manifests on the outside in symptoms like skin rashes and acne.  

Digestion is a crucial biological function that helps our bodies to detoxify and eliminate any waste or problematic byproducts (including excess hormones). “When someone is not having regular bowel movements, their digestion is off, their liver is overwhelmed, or other combinations, the skin may be utilized in a greater capacity to get rid of metabolic and hormonal by-products,” Dr. Schuff explains. This can lead to an imbalance in skin health that shows up as acne and other skin issues.

How Do Imbalances in the Main Hormones Affect Your Gut?

Different hormones impact the balance of your microbiome in different ways. When these secret agents of health are humming along at balanced levels, they have a healthy and symbiotic relationship with your gut. But when an imbalance on either side occurs, they can create problems including leaving you feeling rundown.

Estrogen, Testosterone, and Progesterone

These three may be infamous for their role as sex hormones, but they also have a significant impact on the workings of your gut. High levels of estrogen and progesterone have been shown to reduce the speed at which food moves from your stomach into your small intestine, which can cause bloating. Increased estrogen additionally affects how your intestines then process that food, slowing the whole system down and leading to constipation. “This is why some women may notice a cyclical nature to their constipation,” says Dr. Vincent Pedre, author of Happy Gut.

While testosterone on its own doesn’t have the same effect, these hormones don’t work in isolation. An imbalance in one can throw one or all of the others out of balance.


Insulin is arguably the biggest player in our metabolic health,” says Dr. Schuff. It’s responsible for managing blood sugar, regulating inflammation, as well as restoring and reserving resources in the body. When your blood sugar is consistently high, it can start to overwhelm the system by messing with your body’s finely tuned balance of insulin regulation, leading to insulin resistance, and causing health problems including diabetes.

“Insulin resistance is caused by a gut bacterial imbalance from the overgrowth of bad bugs that scramble your insulin signal,” says Dr. Pedre. This in turn, he explains, can affect your other hormones, such as causing increased estrogen production from fatty tissue.


Cortisol is famous for the part it plays in our stress response. When things are good, they’re really good. “Along with melatonin, cortisol regulates our daily circadian rhythm, which helps us feel awake and alert in the morning and sleepy and relaxed at night,” Dr. Pedre says.

But when your cortisol is high, particularly when it stays high for an extended period of time due to chronic stress, it can cause a series of meltdowns centered in the gut.

As part of the fight or flight response, elevated cortisol sends a signal to start conserving and mobilizing resources to address the emergency. This includes sending blood to our brain, muscles, and limbs instead of our digestive organs. If cortisol levels remain elevated and this signal is consistently repeated, it can knock your digestion and gut microbiome out of balance. “In other words, when we are in a stressed state, the body doesn’t prioritize digestion,” Dr. Schuff says.  

These gut issues are further compounded by high cortisol’s effect on sleep issues, which can lead to a whole host of problems including carb and sugar cravings. “The gut becomes a secondary bystander from excess carb and sugar intake, leading to dysbiosis,” Dr. Pedre says.

Thyroid Hormones

Thyroid hormones control your metabolism rate, with thyroid receptors found on nearly every tissue and cell in the body. Like the larger gut-hormone story, the influence of these hormones on your gut goes both ways. When you are producing too little or too much thyroid hormone — hypothyroidism and hyperthyroidism, respectively — one symptom is a digestive system that either speeds up or slows down in very unwelcome ways.

But the trigger for a thyroid hormone-gut breakdown can also go the other way. When your microbiome is disrupted, it can affect your body’s ability to produce thyroid hormone, causing hypothyroidism, according to Dr. Schuff.

Melatonin & Serotonin

Often called the “sleep hormone,” melatonin is released by the pineal gland when it gets dark at night. But it does more than just help you sleep. “Fun fact: 400x more melatonin is actually produced in your gut than your brain,” says Dr. Pedre. “It regulates the rhythmic movement of the intestines and inflammation.”

Melatonin doesn’t work completely on its own. To successfully produce this hormone, you also need the “happy hormone” serotonin. “Serotonin is thought to be a brain-based chemical (think of SSRI antidepressant medications) but interestingly more than 90% of our serotonin is produced from our gut-microbiome,” Dr. Schuff says. “If our gut is out of balance and digestion is skewed, it could be that serotonin production and release could be impaired as well.” This, says Schuff, can affect sleep, mood, concentration, and the production of our sleepy hormone, melatonin. 

So, How Can You Keep Everything Zen and Balanced?  

While hearing all the ways that gut dysbiosis can occur may be daunting, there are plenty of things you can do to keep your body in balance. Some of the best lifestyle practices to support both a healthy gut microbiome and hormonal balance are:

  1. Eat real food: “Our gut-microbiome responds to every single thing we consume so we are literally making a decision about its health, balance, and integrity with every bite we take,” Dr. Schuff says. Eating a whole foods-based diet will make you less likely to disrupt your blood sugar balance and develop a metabolic disorder which could affect your hormones. Prioritize colorful vegetables and fruits. “The soluble and insoluble fiber in vegetables especially feed the gut-microbiome to build a robust and diverse microbial community,” Dr. Schuff says.

  2. Eat healthy fermented foods: Things like kimchi, sauerkraut, and kombucha contain beneficial bacteria that help rebalance the gut. A study done by Stanford University showed that a high fermented foods diet increased gut microbiome diversity and lowered nineteen inflammatory markers in comparison to a fiber-rich diet.

  3. Ditch the sugar: “Sugar is a known hormone-disruptor and it can increase inflammation in the gut, as well as allow sugar-eating bacteria and yeast to overgrow and crowd out beneficial probiotics,” says Dr. Pedre. If you want better hormone balance through a healthier gut, try to eliminate sources of added and refined sugar in your life.

  4. Drop the commercial dairy: “Hormones and antibiotics fed to dairy animals can sometimes be found in dairy products and can result in the recirculation of toxins and estrogen in the body,” says Dr. Pedre. Choose raw, unpasteurized dairy, which is rich in enzymes, or opt for nut milks and other non-dairy options.

  5. Audit your environment: “Could you be exposing yourself to problematic chemicals disturbing hormonal and gut-microbiome balance daily without knowing it?” asks Dr. Schuff. The answer is yes. Women are especially sensitive to endocrine-disrupting chemicals in common products because of their menstrual cycles, as well as the high levels of hormone disruptors found in many beauty products. Dr. Schuff recommends taking stock of what you are regularly exposed to and using resources like the Environment Working Group to find alternatives if necessary.

  6. Move: “Daily movement has a myriad of positive effects, not least being to help your bowels and digestion moving along and get rid of hormones and other metabolic by-products,” says Dr. Pedre.

  7. Sleep: “Sleep deprivation disrupts metabolism, digestion, hormones and contributes to stress,” Dr. Pedre explains. If you aren’t sleeping well, try some tactics to start improve your sleep quality.

  8. Hydrate: “Drink more water to keep digestion moving and prevent constipation,” says Dr. Pedre. He also recommends eating a combination of soluble and insoluble fiber. Most people, he says, consume less than a third of the daily recommended amount of fiber. For women, it’s 25-35 grams daily, and for men, it’s 35 - 45 grams daily. “Fiber helps move stool through the digestive tract, but also aids in the elimination of metabolized hormones and toxins,” says Dr. Pedre.

  9. Calm down and lower stress: “Chronic stress has proven to have detrimental effects on gut and hormone health,” says Dr. Pedre. While it can be frustrating to hear “lower your stress” as the response to almost every ailment, it’s offered so often for a reason. Figure out what practices work to help you wind down and decrease your stress and start scheduling those activities into your day.

Want to learn more about the connection between your gut and your hormones? Send us an email at [email protected].

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