Balance Your Hormones by Stabilizing Your Gut

Balance Your Hormones by Stabilizing Your Gut |Women's Health|Sara Gottfried MD

Your hormones exist in a delicate balance, playing alongside one another like instruments in an orchestra. Throughout the day your hormones fluctuate in rhythms, like crescendos of a symphony. Each hormone is like a specific instrument that must play on time and in rhythm with your other hormones. Together, your hormones create a beautiful harmony – your stable sense of wellbeing.

This is more than just an analogy – your hormones affect everything about you. They drive what you’re interested in. From your mood to your satisfaction, motivation, hunger, metabolism, happiness, and more – all of these are deeply influenced by your hormones.

Whenever one of your hormones is out of tune, you feel it. Your rhythm and flow are affected. Eventually, a hormone out of rhythm affects those it interacts with and can set off a cascade of negative consequences. Because of the interconnectedness of your hormones, you can go from feeling totally fine one day to feeling completely off the next.

The endocrine system is the collection of organs responsible for your hormones. When people think of hormone producers, they usually think of glands throughout the body like the thyroid, adrenals, and reproductive organs.

But the gut microbiome may be the most important organ of the endocrine system – and it is often overlooked.[1] In fact, the gut microbiome may be more important than the other hormone-producing glands in your body. Why?

Your Gut Microbiome Regulates Your Hormones

If your hormones are like a symphony, then your gut microbiome is the conductor. Your gut microbiome regulates your hormones carefully. When your gut microbiome is healthy, it does its job well. But when it is unhealthy, it throws your hormones out of tune and can cause all sorts of problems.

Women are especially impacted when hormones are thrown off balance. Common hormone disorders in women include:

  • Hypothyroidism
  • Autoimmune thyroid disorders including Hashimoto’s thyroiditis and Grave’s disease
  • Polycystic ovary syndrome
  • Estrogen dominance, including low progesterone
  • Perimenopause
  • Menopause
  • Stress-related fatigue (dysregulation of the hypothalamic-pituitary-adrenal or HPA axis)
  • Low testosterone
  • Low estrogen
  • Osteoporosis
  • Endocrine disruption from toxins
  • Hyperthyroidism

Your gut microbiome plays an important role in most of these conditions. The various roles of the gut microbiome within in the endocrine system include:

  • Synthesizing and secreting most hormones
  • Regulating the expression of these hormones
  • Inhibiting the production of certain hormones in other organs of the body
  • Enhancing production of hormones throughout the body

This means your gut microbiome isn’t just producing hormones, it’s also telling the other glands in the body how much or how little of each hormone they should be creating and releasing.

What are some of the specific hormones controlled by the gut microbiome?

How Hormones Are Impacted by Your Gut Microbiome

While your gut microbiome regulates your hormones in some way or another, there are 4 neurohormones that deserve mention.

  1. Melatonin
  2. Norepinephrine and epinephrine
  3. Estrogens
  4. Thyroid hormones

Let’s take a closer look at how the gut microbiome is critical to your body’s use of these 4 hormones.

Your Gut Microbiome Helps Create Melatonin

Did you know scientists have found that your gut microbes are responsible for producing 90% of your serotonin neurotransmitter?[2] Serotonin gets most of its attention for being the “happy chemical,” but it also has other important roles. One such role is acting as the precursor to another important hormone, melatonin.

Melatonin is extremely important to maintaining your sleep-wake cycles and other internal clocks. Without the right microbes making serotonin, you won’t get enough melatonin, which can make it difficult to fall asleep, stay asleep, and maintain a level of calmness.

Your schedule impacts your gut microbes, and vice versa. Studies have found specific bacteria such as Enterobacter aerogenes are sensitive to melatonin rhythms. As melatonin is secreted from the gut lining, it can cause an increase in Enterobacter aerogenes. This suggests our circadian rhythms may be regulated more closely alongside specific bacterial clocks than we previously realized.[3]

The Gut Microbiome Can Raise Stress Levels

Norepinephrine and epinephrine are two hormones often associated with our fight-or-flight response. When these hormones are increased in the body, they cause an acute stress response, which leads it:

  • Increased heart rate
  • High blood pressure
  • Increased cardiac output
  • Higher blood glucose levels
  • Anxiety
  • Stress

While you need some norepinephrine and epinephrine to keep you safe in an emergency, too much for too long can cause stress, anxiety, and depression. It can be miserable to feel overly anxious with no real reason behind it. Not only that, certain bacteria have been associated with higher levels of norepinephrine and epinephrine.

E. coli, Salmonella, and Pseudomonas have all been associated with prolonged high levels of norepinephrine and epinephrine in the body. What’s worse is once these harmful bacteria have a stronghold on your gut microbiome, some of the microbes sense the epinephrine hormones and it triggers their virulence gene expression – making them even more potent and powerful.[4]

The effect of chronic stress on the gut is bidirectional. The hormone that releases the stimulus for cortisol, corticotropin releasing hormone (CRH), can poke holes in the gut lining, leading to increased intestinal permeability.[5] The process is mediated by mast cells in the gut wall.[6]

How the Gut Affects Estrogen Levels

You actually produce three main forms of estrogen – estrone, estradiol, and estriol. Though these are often associated with women, estrogens aren’t just created by female reproductive organs. Estrone, estradiol, and estriol are also generated by the gut microbiome. In fact, a healthy microbiome produces more estriol. For a long time estriol wasn’t given much attention because it’s the weakest of the three. It was believed to be only present during pregnancy, which we now know is not the entire story.

The other two estrogens were much “louder” – meaning more biochemically potent when they bind to an estrogen receptor – so they got most of the attention. It turns out that because estriol is weak, it’s incredibly beneficial to the body. Basically, you get the benefits of estrogen with estriol (i.e., strong bones) without as many negative effects (i.e., breast cancer). A healthy gut microbiome produces beneficial estriol and maintains a healthy balance of the other estrogen metabolites.

Not only does your gut microbiome help create more estriol and maintain estrogen balance overall, a specific group of microbes called the estrobolome reduces harmful side effects of more potent estrogen. Your estrobolome helps metabolize excess estrogen to keep it from causing problems.[7] That’s great news because too much estrogen can cause weight gain, mood issues, painful menstrual cycles, and potentially breast, endometrial, and prostate cancer.

Your gut microbiome not only produces estrogens, but also tells your body to increase its own production when necessary, while metabolizing any excess estrogens. This is another example of how research is demonstrating that your gut microbiome is one of the conductors of your hormonal orchestra, keeping everything in sync and in tune.

Beyond the Thyroid: Your Gut Microbiome’s Role

Your thyroid is another endocrine gland that is critical to your wellbeing. When your thyroid levels are off, doctors usually look to correct your… well, your thyroid. But research suggests that it’s a good idea to check the gut before the thyroid for any imbalances. Studies are showing that altered gut microbiome compositions are associated with varying thyroid conditions.

In particular, low microbial diversity has been correlated with high levels of thyroid stimulating hormone (TSH).[8] High TSH levels can lead to the overproduction of T3 and T4  thyroid hormones. High T3 and T4 can cause hyperthyroidism and make you feel anxious, jittery, and cause unexplained weight loss.

Eventually, if you have hyperthyroidism that goes untreated for a long time, it can lead to hypothyroidism as your thyroid becomes overworked. As you can probably imagine, hypothyroidism occurs when thyroid hormone levels are low. Hypothyroidism is also associated with alterations in the gut microbiome.[9] It causes fatigue, intolerance to cold, and weight gain.

Anyone who has experienced the swing in thyroid conditions can tell you that going from hyperthyroidism to hypothyroidism can make you feel like your life is on a rollercoaster. But what if the best solution was to heal the gut first and foremost?

Bottom Line? Unbalanced Hormones Begin in the Gut

The discovery of the gut microbiome occurred after most doctors today finished medical school. Because of this, the gut microbiome is a vital organ still missing from many endocrine system models.

If you are dealing with any conditions relating to hormonal balance, gut health must be a priority. When you try to restore balance to your hormones, you need to first restore balance to your gut microbiome.

How to Know if Your Gut is Out of Balance

Here is a simple questionnaire that can alert you about problems that you may have with dysbiosis or leaky gut. (For a questionnaire on hormone balances, check out my free hormone quiz.)

In the past 6 months, have you experienced . . .

  • Gas, bloating, abdominal discomfort on most days?
  • Chronic diarrhea, constipation, or both?
  • Fatigue or low energy on most days?
  • Chronic stress?
  • Brain fog, decreased cognitive function, or slow processing speed?
  • Carbohydrate intolerance, particularly fiber or beans?
  • Itching of the vagina or anus?
  • Stomach bugs or history of traveler’s diarrhea?
  • Depression or anxiety?
  • Sinus congestion and/or bad breath?
  • Use of antibiotics?
  • Diagnosis of reflux, heartburn, and/or use of antacids?
  • Food sensitivities, such as gluten or dairy?
  • Exposure to toxins, such as glyphosate in genetically-modified foods or mercury from dental fillings or contaminated seafood?
  • A diagnosis of an autoimmune condition, such as Hashimoto’s thyroiditis or psoriasis?

If you answered “yes” to 5 or more questions, you may have a problem with your microbiome, and by extension, your hormone balance. I recommend further testing, and importantly, to work with a knowledgeable functional medicine practitioner who is experienced with gut recovery.

While there isn’t a single test that does it all, here is a brief overview of a few of the gut tests that I commonly use in my practice, depending on the individual and symptoms. I’ll describe more about these tests in a future article.

  • Microbiome testing, such as Viome or the American Gut Project. Note that both of these tests are direct-to-consumer and informational, meaning they do not diagnose disease or provide medical advice. However, a wise practitioner familiar with the tests can provide insights and recommendations. I am still vetting both tests as their technology is complex, particularly as they relate to hormonal balance.
  • Microbiota testing, such as from Ubiome, although I find these data to be very limited.
  • Breath testing for small intestinal bacterial overgrowth (SIBO). Read more about breath testing for SIBO in this excellent review.
  • Organic Acid Test, from Great Plains Lab, or Precision Analytical, which also offers hormone and metabolism testing.
  • Microbial assay and biomarker testing, such as the GI-MAP.
  • Occasionally I perform a comprehensive stool analysis but less often given the better technology used in the tests mentioned previously.

Next Step: Restore Gut Balance

In summary, research suggests that gut microbial balance is key to hormonal balance.[10, 11] The gut appears to play a major role in coordinating homeostasis or balance in the neuroendocrine and immune systems.

Since the gut microbiome is one of the most important organs involved in the effort to balance your hormones, it should be part of your future protocols. Why? Because the gut microbiome creates, breaks down, changes the expression of, and tells the body to make more or less hormones, and then how to use them. It works bidirectionally with another brain/body control system for your hormones, the hypothalamic-pituitary-adrenal-thyroid-gonadal (HPATG) axis—which I’ve written about extensively in all of my books, starting first with The Hormone Cure.

For more information on how to restore gut balance, tune into my future articles on best practices for testing the microbiome and its activity, plus the key role of diet, macronutrients, micronutrients, chronic stress, supplements, prebiotics, probiotics, and other solutions.

If you’re a practitioner who wants to learn more about how to create sustained hormone balance in your patients with science-backed protocols that include the microbiome, register here.

Remember – Your gut microbiome is one of the conductors of the complex hormonal orchestral playing throughout your body. Your gut microbiome regulates your hormones and for your hormones to be balanced, your gut microbiome should be balanced.



[1] Clarke, G et al. “Minireview: Gut microbiota: the neglected endocrine organ.”  Mol Endocrinol. 2014 Aug;28(8):1221-38.

[2] Yano, J et al. “Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis.” Cell. 2015 Apr 9; 161(2): 264–276.

[3] Paulose JK, et al. “Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity.” PLoS One. 2016 Jan 11;11(1):e0146643.

[4] Moreira, C, et al. “Bacterial Adrenergic Sensors Regulate Virulence of Enteric Pathogens in the Gut.” mBio.00826-16 7 June 2016 mBio vol. 7 no. 3 e00826-16.

[5] Brozozowski B, et al. “Mechanisms by which Stress Affects the Experimental and Clinical Inflammatory Bowel Disease (IBD): Role of Brain-Gut Axis.” Curr Neuropharmacol. 2016;14(8):892-900.

[6] Vanuystel, T et al. “Psychological stress and corticotropin-releasing hormone increase intestinal permeability in humans by a mast cell-dependent mechanism.” Gut. 2014 Aug;63(8):1293-9. doi: 10.1136/gutjnl-2013-305690. Epub 2013 Oct 23.

[7] Kwa M, et al. “The Intestinal Microbiome and Estrogen Receptor-Positive Female Breast Cancer.” J Natl Cancer Inst. 2016 Apr 22;108(8). doi: 10.1093/jnci/djw029. Print 2016 Aug.

[8] Zhou L, et al. “Gut microbe analysis between hyperthyroid and healthy individuals.” Curr Microbiol. 2014 Nov;69(5):675-80. doi: 10.1007/s00284-014-0640-6. Epub 2014 Jun 27.

[9] Zhao F, et al. “Alterations of the Gut Microbiota in Hashimoto’s Thyroiditis Patients.” Thyroid. 2018 Feb;28(2):175-186. doi: 10.1089/thy.2017.0395. Epub 2018 Feb 1.

[10] El Aidy S, et al. “Gut Microbiota: The Conductor in the Orchestra of Immune-Neuroendocrine Communication.” Clin Ther. 2015 May 1;37(5):954-67. doi: 10.1016/j.clinthera.2015.03.002. Epub 2015 Apr 3.

[11] Neuman H, et al. “Microbial endocrinology: the interplay between the microbiota and the endocrine system.” FEMS Microbiol Rev. 2015 Jul;39(4):509-21. doi: 10.1093/femsre/fuu010. Epub 2015 Feb 19.