How the Gut Affects Hormone Balance

February 2023

By Ali Kucich Brady, MSc, FNLP, FNTP, BCHHC, CHSC, Owner of Eighty Nutrition, Functional Medicine Nutritionist


These days, gut health dominates talk in the wellness world. We read again and again that a healthy gut is imperative for good health and that we should consider what we are eating for improved gut health. But, apart from good digestion, why does gut health matter and how is it linked to hormonal and overall body health?

The gut, technically the gastrointestinal tract, or our “digestive system,” is one of the most intricate and complex systems in the body. A universe unto itself, the gut contains trillions of microbes, known collectively as the “gut microbiome.” The gut microbiome is home to countless species of bacteria, yeast, fungi, and viruses that play a critical role in modulating our body’s immune response, brain function, and metabolism. It’s also where we produce and regulate many essential hormones and neurotransmitters, metabolize nutrients, and neutralize pathogens. The digestive tract provides our body with natural defenses against bacteria, viruses, and parasites in the form of stomach acid, digestive enzymes, and bile.

Poor gut health can play a role in altering our inflammation level, cancer risk, sugar metabolism, and immune system. Research shows that 70-80% of our immune system is directly connected to the GI tract. Some of the primary reasons for an altered gut microbiome include gut dysbiosis (imbalanced gut bacteria), intestinal permeability (colloquially known as “leaky gut”), and nutrient deficiencies.

Chronic gut issues often manifest as:

  • Bloating and gas
  • Diarrhea, constipation, or a combination of both
  • The feeling of acid reflux (from high or low stomach acid)
  • Headaches
  • Chronic fatigue
  • Food sensitivities
  • Skin rashes, eczema, and/or hormonal acne
  • Food cravings
  • Depression and anxiety
  • Autoimmune conditions

A significant number of hormones are produced or modulated by microbes in the GI tract, including those related to mood, fertility, and metabolism. If your goal is to optimize gut health and keep hormones in balance, consider these links between your gut health and your hormones.

Serotonin Production

Serotonin is one of the major ways that gut health influences our mental state. Research shows links between inflammation in the gut microbiome and mental illness, including anxiety and depression. Around 90% of our body’s serotonin, often known as the “happy hormone,” is produced in the gut. When serotonin is at normal levels, we feel more focused, emotionally stable, happier, and calmer. Conversely, low levels of serotonin are associated with depression and anxiety. Serotonin is synthesized (made) from tryptophan. Often, tryptophan depletion is seen in those with mood-related conditions, such as depression and anxiety. One way we can increase our body’s serotonin levels is to eat tryptophan-rich foods, such as eggs, seeds, nuts, lean meat, cheese, and lentils.

Melatonin Production

If you are low in serotonin, you are also low in melatonin. Melatonin, which we all know as the sleep hormone, is synthesized from serotonin in the brain’s pineal gland. Serotonin produced in the gut throughout the day is the precursor to melatonin made at night. In addition to improving sleep, melatonin is also involved in managing immune function, blood pressure, and cortisol levels. Plus, it acts as an antioxidant, with some research showing that it can significantly affect many health conditions. Without enough serotonin from the gut, melatonin production all but ceases.

GABA (Gamma-aminobutyric acid)

Gut bacteria significantly influences the communication between the brain and the gut. When the gut is full of healthy bacteria, it has the potential to regulate mood, as seen with GABA. GABA is a neurotransmitter that reduces neural activity in the brain, reduces feelings of stress, and improves sleep and relaxation. Low levels of GABA are linked to depression and mood disorders. Beneficial bacteria in the gut have been clinically shown to increase GABA receptors in the brain, and help alleviate several mood disorders. Plus, recent research suggests that the gut microbiota, specifically Bifidobacterium and Lactobacilli strains, can produce GABA, influencing the gut-brain axis response, and reducing anxiety and depression-like behavior. A simple way to increase GABA is to include more GABA-producing foods in your diet, such as broccoli, potatoes, sweet potatoes, lentils, berries, wild-caught fish, and grass-fed beef. Fermented foods and foods rich in vitamin B6 will also help to increase GABA levels. Include foods rich in probiotics such as fermented pickles, sauerkraut, kimchi, and plain kefir, as well as foods that boost B6, such as spinach, garlic, Brussels sprouts, and bananas.

Estrogen Regulation

There has been a recent influx of research indicating that the gut microbiome plays a large role in estrogen regulation. Research indicates that poor gut health increases the risk of estrogen-related disorders and illnesses, such as PCOS(Polycystic Ovary Syndrome), endometriosis, and even breast cancer. Our gut microbiota can determine how well we detoxify and excrete estrogen. Research points to a specific type of microflora, known as the “estroblome,” that helps to regulate levels of estrogen. Gut microbiota in the estroblome regulate estrogens through the secretion of an enzyme called β-glucuronidase. People with gut dysbiosis or low gut microbial diversity are likely to end up with less active estrogen circulating, as well as “dirty” estrogen metabolites being reactivated and recirculated throughout the body. This recirculation of undesirable estrogen waste products can cause issues with estrogen dominance and manifest itself in PMS symptoms and adrenal dysfunction. Studies show that many breast cancer patients show poor overall microbiome health, which may be a factor in the development of the disease.

Low Thyroid

Gut microbiota influences our body’s ability to assimilate and absorb key micronutrients such as iodine, selenium, zinc, iron, B vitamins, vitamin A, and tyrosine, all of which are essential to healthy thyroid function. Approximately 20% of thyroid hormone conversion from inactive T4 to active T3 occurs in the gut. Research shows that a deficient thyroid can lead to other gut dysfunction symptoms, like nutrient deficiencies, and bacterial and fungal overgrowth.

Blood Sugar Regulation

Recently, research has indicated that the gut microbiome might be an important contributor to the development of insulin resistance, obesity, and type 2 diabetes. Metabolic dysfunction has been directly linked to gut dysbiosis and intestinal permeability. Intestinal permeability creates inflammation, which in turn reduces a person’s insulin sensitivity, and can lead to the development of more severe metabolic disorders. Studies show that the gut microbiomes of obese individuals have fewer short-chain fatty acids, and a differential proportion of particular bacterial species in their gut microbiota: fewer Bacteroidetes and more Firmicutes. Additionally, the fat-storage hormone insulin is in part regulated by Lactobacillus reuteri, which lives in the gut.

So how can we improve our overall gut health and achieve hormonal balance?

Our first step is to begin with a nutrient-dense, anti-inflammatory diet that supports a balanced gut microbiome. This includes eating a diverse range of proteins and high-quality fats, as well as vegetables and brightly-colored fruits, which are high in fiber and phytonutrients to encourage microbial diversity. Prebiotic foods, such as garlic, onion, asparagus, and bananas provide the material that gut bacteria like to feed on. Probiotic foods, such as kefir, tempeh, sauerkraut, kimchi, and other fermented foods are really useful for introducing beneficial bacterial strains, like Lactobacillus, to the gut. Because the biggest cause of an unhealthy microbiome is a diet high in sugars, alcohol, processed foods, and seed oils, reducing these foods can also make an impact.

It’s also important to focus on the body’s needs for optimal digestion, including sufficient digestive enzymes, stomach acid, and bile acid. Occasionally, it is necessary to supplement to ensure we have adequate supply, especially as we age past forty. If you work through the suggestions offered here and still feel “off”, we recommend functional lab testing from a functional medicine practitioner or naturopathic doctor, as an option for digging even deeper into your own unique blueprint.


Ali is a board-certified functional medicine nutritionist and health coach, who helps clients optimize their hormonal health, restore their gut microbiome, and reduce inflammation with nutrition and lifestyle interventions. Her private practice, Eighty Nutrition, has helped hundreds of people achieve their peak state of awesome… mind, body, and soul.

Ali’s journey into the world of functional nutrition began twenty years ago when she was battling chronic health challenges that left her fatigued, sick, and in pain. In recovering her health, Ali came to understand that food and lifestyle interventions were at the core of optimal health and were the key to enhanced energy, healthy body composition, and overall wellness.

Ali holds degrees from Franklin & Marshall College, The London School of Economics, and Tufts University’s Friedman School of Nutrition Science and Policy. She has certifications from The Functional Nutrition Alliance, The Nutritional Therapy Institute, The Institute for Functional Medicine, and The Natural Gourmet Institute of Health and Culinary Arts. Ali has specialized training in functional hormonal health, autoimmune protocols, therapeutic nutritional supplementation, and functional blood chemistry analysis.

Ali supports clients across the country with science-based, 1:1 concierge-style nutrition protocols, as well as her seasonal group programs, the Real Food Reset and the 6-week bootcamp to break through bad habits and fad diets.