Common Hormone Problems That Actually Begin in Your Gut

How you think and feel every day is closely tied to your hormone health…but what controls your hormones? Ultimately, many hormone problems can begin in the gut. This is because the gut microbiome–the trillions of bacteria that live in our digestive system–plays a huge role in regulating hormones. When the gut microbiome is unhealthy, it can cause problems like estrogen-related diseases, thyroid problems, PCOS or endometriosis, and type 2 diabetes. Luckily, there are steps we can take to improve gut health and regulate hormones. In this blog post, we will discuss 5 hormone problems that start in the gut and the ways we can improve our gut health and hormones!

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How the gut-hormone connections affects your body

As recently as 20 years ago, scientists believed that what happened in the gut, stayed in the gut, but now we know that your microbiome’s influence extends to almost every other body system, including your hormones. Consider this:

Your gut controls your mood. Up to 95% of the feel-good hormone, serotonin, is made in your gut (1). Serotonin is a neurotransmitter that carries signals between neurons in the brain. It regulates mood, cognitive function, sleep cycle, and much more.

Gut bacteria help digest food and provide certain nutrients, some of which we can’t make on our own—or not in sufficient quantities—such as vitamin K. Gut bacteria also make some B vitamins, folate, and biotin (2).

A healthy microbiome helps fight off germs and illness. Your gut makes up a large portion of your immune system, helping to distinguish invading pathogens from friendly cells (3). 

Bacteria in the gut regulate metabolism, influencing your appetite, and your ability to gain or lose weight (4).

Every day it seems that scientists discover another function of gut bacteria that goes far beyond the gut. The gut microbiome can affect hormonal balance, cardiovascular health, inflammatory response, and so much more.

Related: Which Probiotic Can Help Shed Belly Fat?

Your gut microbiome plays a key role

The gut microbiome is the community of microbes residing in your gut. These are the beneficial gut bacteria that numbers in the trillions in your gastrointestinal tract. Healthy gut flora includes a whole ecosystem of bacteria, fungi, viruses, and protozoa that have a beneficial (and sometimes detrimental) impact on the human body.

The key to good health and hormone balance is maintaining a balance of “good” and “bad” bacteria.

But poor quality diet, age, environmental toxins, chronic stress, and other factors can contribute to an imbalance of gut microbiota known as gut dysbiosis. Gut dysbiosis is having too much of, or the wrong type of bacteria present in the wrong place.


Related: 5 Rules to Rebuild (+ Maintain) a Healthy Gut

What does an unhealthy gut feel like?

Gut dysbiosis manifests in a variety of ways for different people, and symptoms aren’t always limited to the digestive system. If your gut is unhealthy, it can trigger chronic inflammation that can cause symptoms inside and outside of the gut.

Symptoms of an unhealthy gut vary widely and may include:

  • Frequent gas, bloating
  • Stomach pain/cramps
  • Frequent heartburn
  • Food sensitivities
  • Brain fog
  • Mood disorders, i.e., anxiety, depression
  • Chronic sinus congestion or worse allergy symptoms
  • Diarrhea or constipation
  • Candida overgrowth
  • Acne, rosacea, eczema
  • Headaches
Healthy hormones start in the gut.
Healthy hormones are made in the gut.

Having an unhealthy gut can also put you at risk for certain health problems, such as autoimmune disorders, IBS or IBD, liver disease, or diabetes (5).

Though our gut is regularly exposed to pathogens that would do us harm, the biggest cause of an unhealthy gut is related to lifestyle.

A diet that’s high in sugar, bad fats, and alcohol, in addition to high levels of stress, overuse of antibiotics, and certain medications can all lead to disruptions in healthy gut flora.

Read more: Use This Ingredient to Heal & Seal a Leaky Gut

Poor gut health is linked to estrogen issues

The estrogen in your body is processed by bacteria in the gut, which we call the estrobolome. This estrobolome includes the enzymes responsible for breaking down hormones and healthy bacteria in your gut.

The estrobolome controls how your body breaks down and eliminates excess estrogen hormones after they’ve done their job. This is a process known as estrogen metabolism. 

Dysbiosis in the gut can lead either to a deficiency or excess of estrogen, which can also result in imbalances in other hormones as well.

Diet, lifestyle, and certain medications can affect the healthy function of your estrobolome and estrogen levels. Excess estrogen can cause irregular periods, mood changes, weight struggles, headaches, bloating, and other digestive ailments. These symptoms are common with estrogen dominance.

Read more: How Your Estrobolome Controls Hormone Health


PCOS is a hormonal disorder that can cause missed periods, weight gain, excess hair growth, and acne, and is also one of the main causes of infertility. Women with PCOS have a higher rate of gut dysbiosis than women who do not have PCOS (6). 

There’s also evidence to suggest that changing the composition of gut bacteria can help alleviate some of the common symptoms of PCOS, such as high androgens and irregular periods (7). 

Read: Is PCOS Responsible for Your Leaky Gut? 


Endometriosis is a painful condition in which the tissue that lines the inside of your uterus (the endometrium) starts to grow outside of it. Symptoms are worsened by excess estrogen, which can result from a dysfunctional estrobolome.

Poor estrobolome function (estrogen metabolism) in the gut is common with endometriosis, and may also be linked to an unhealthy vaginal microbiome as well (7,8)

Ovarian, breast and cervical cancers

There is a strong link between gut dysbiosis and various types of cancer, especially ovarian, breast, and cervical cancers. The gut microbiota metabolizes estrogen to prevent it from recirculating in the blood and increasing the risk for estrogen-sensitive cancers. So the estrobolome is a key part in ridding the body of harmful excess estrogen (9). 

A healthy gut microbiome is also important for maintaining a healthy immune system, which is your body’s first line of defense against cancer. An unhealthy gut can lead to chronic inflammation, which is a risk factor for the development of cancer.

Thyroid problems

The gut-thyroid connection might be the most sensitive out of all the hormone-related problems that begin in the digestive system. Gut dysbiosis is incredibly common with autoimmune thyroid diseases like Hashimoto’s, in addition to some types of thyroid cancer. 

Certain gut bacteria also help process nutrients necessary for the conversion of T4 to T3—such as selenium and zinc. Gut dysbiosis inhibits this process, which may result in symptoms of low thyroid like fatigue and weight gain. Altered composition of gut bacteria is also associated with high TSH levels. If you have too much TSH, your body may also produce lower levels of both T3 and T4 (10). 

These thyroid hormones affect every tissue in your body and perform several essential functions. And when your thyroid isn’t working properly, it’s important to get into a qualified holistic practitioner as soon as possible.

Read: Is It Perimenopause or a Thyroid Problem?

Estrogen and diabetes

There is a strong link between gut dysbiosis, estrogen issues, and type II diabetes. Gut dysbiosis has been linked to insulin resistance, which is a major precursor for developing type II diabetes (11). In fact, researchers have found significant differences in the amount and type of bacteria present in the microbiome of those with type II diabetes versus those who don’t have diabetes.

Type II diabetes is a condition that’s characterized by high blood sugar levels and chronic, low grade inflammation. It’s often caused by diet and lifestyle factors, such as a poor diet and being sedentary.

Explore: 5 Fresh Summer Desserts That Won’t Wreck Your Hormones!

Restore Hormone Balance with a Healthy Gut

Much of what controls whether your gut is healthy—or in a state of unhealthy inflammation—comes from your daily habits, diet, and how you treat your gut. The key takeaway is that a healthier gut means better hormone balance and a happier you.

You can build or maintain a healthy gut by eating healthy foods that are good sources of pre- and probiotics, such as fermented foods and nutrient-dense fruits and veggies. Then, you’ll want to remove some of the detrimental items like ultra-processed foods and alcohol. It also helps to address your stress levels, as this can influence your digestive system and hormone balance as well.

Rebuild and maintain a healthy gut with the help of Belly Fix, a daily boost of gut-healthy probiotics, fermented superfoods, and digestive greens.

Follow these tips for a healthy, balanced gut:

Choose foods high in prebiotic fiber

Vegetables, fruits, nuts & seeds, and some grains are great sources of fiber that provide fuel for healthy gut bacteria, such as:

  • Garlic
  • Onions
  • Leeks
  • Asparagus
  • Chicory root
  • Jerusalem artichoke
  • Apples
  • Cacao (raw cocoa)
  • Flax seeds and hemp seeds
  • Oats and barley

Try incorporating a couple of these foods into your diet at a time to support a healthy microbiome. The important thing to remember is that ultra-processed foods and high sugar diets don’t help to restore gut health. 

Eat more anti-inflammatory foods

Chronic inflammation is one problem area for an unhealthy gut and hormonal imbalances, and the food you eat can calm or worsen this inflammation.

Omit bad fats like vegetable oils, swapping instead for healthy fats from fish, avocados, coconut, or olive oil. You can also eat more antioxidant-rich foods like berries, leafy greens, and quality proteins.

Add fermented and cultured foods

Fermented foods contain active healthy bacteria called probiotics that help balance your overall gut microbiome. A balanced gut microbiome is important for hormonal balance. Yogurt, sauerkraut, kimchi, kombucha are sources of good probiotics.

Take a probiotic supplement

S. boulardii has been shown to be particularly helpful to combat the effects of dysbiosis and destroy the protective mechanisms (called biofilms) that bad bacteria use to disguise themselves from your immune system. 

Taking a probiotic may also help with proper nutrient absorption, which is critical to rebuilding and maintaining a healthy gut. Probiotic products promote the growth of good bacteria in your digestive tract as well as supporting immune health within your intestinal tract.

Read: How to Choose the Best Probiotic for Digestive Health, Weight Loss, and More

The takeaway

So, what can you do to restore a healthy gut and balance your hormones? First and foremost, improve your diet. Eat plenty of fiber-rich fruits and vegetables, as well as fermented foods like sauerkraut, kimchi, yogurt, and kefir. Reduce or eliminate processed foods and sugar. Address chronic stress with techniques like yoga or meditation. And lastly, if needed, take a probiotic supplement to help repopulate the gut with healthy bacteria. When it comes to hormone health, don’t forget about the gut!