The Ultimate Guide to Gut Health for Hormonal Balance

In recent years, there has been a huge surge of interest in gut health. We now understand that dysbiosis—imbalances in your gut microbiome—is linked to a diverse array of health issues, ranging from inflammatory bowel disease to diabetes and even cancer.

This means that many of your hormone-related frustrations—bloating, skin issues, mood swings, and period pain—may be related to your gut health. In this guide, we’ll delve deep into the role of gut health for hormonal balance and outline clear, actionable strategies to reclaim your hormonal harmony.

Estrogen 101

To begin, let’s briefly discuss estrogen.

“Estrogen” refers to a group of chemically similar molecules that play a major role in the female reproductive system. The 3 major forms of estrogen are:

• • Estrone (E1): The primary form of estrogen produced by the ovaries post-menopause.
  • Estradiol (E2): The major (and most potent) form of estrogen produced by the ovaries in pre-menopausal women.

Estriol (E3): This form is primarily found during pregnancy because it’s produced in large quantities by the placenta.

Estrogens work closely with progesterone, another female reproductive hormone, to ensure optimal function in your body. This means that it is of utmost importance to ensure that we maintain a balance between them.

Unfortunately, achieving this balance is difficult for many women, and a prolonged imbalance can lead to unfavorable health effects.

So what does this have to do with gut health?

One thing we’ve learned in recent years is that your gut is in a constant, intricate conversation with your hormones.

The Estrobolome: The Gut-Hormone Connection

Your body is brilliant. It’s true! So brilliant, in fact, that it has a special group of gut microbes dedicated to estrogen regulation — it’s called the estrobolome.

Certain bacteria in the estrobolome produce enzymes that help your body break down estrogen. This means the estrobolome plays a key role in regulating how much estrogen stays circulating in your system.1

In other words, the estrobolome plays a pivotal role in estrogen detoxification.

The Estrobolome and Estrogen Detoxification

The process of estrogen detoxification relies on two major organs:

• The Liver (Conjugation): When the liver is finished using or processing estrogen, it packages the hormone for elimination by attaching a chemical tag (like glucuronic acid or sulfate) in a process called conjugation. This package is ready to be safely excreted via bile into the digestive tract.
• The Gut (Deconjugation/Excretion): Once in the gut, the estrogen package must be promptly eliminated in the stool. A healthy estrobolome ensures this happens.2

However, when there is dysbiosis in the gut, certain bacteria within the estrobolome become overactive. These bacteria produce high levels of an enzyme called beta-glucuronidase. This enzyme deconjugates the package the liver created, allowing the estrogen to become unbound, active, and fat-soluble again.3

This active estrogen is then reabsorbed across the intestinal wall back into the bloodstream. This recirculation elevates overall estrogen levels, leading to estrogen dominance—the primary cause of many common hormonal symptoms, such as:

• Fibroids, endometriosis, or ovarian cysts
• Fatigue
• PMS
• Fibrocystic breasts
• Irregular menstruation
• Unexplained weight gain

This mechanism underscores why prioritizing gut health for hormone balance is essential.

Beyond Estrogen: Your Gut’s Effects on Inflammation and Absorption

Your gut’s influence extends beyond estrogen metabolism:

• Nutrient Absorption: A compromised gut lining or dysbiosis leads to poor nutrient absorption.4 If you’re not absorbing essential cofactors like magnesium, B vitamins, and zinc, your body cannot produce or regulate hormones efficiently. Zinc, for instance, is critical for ovarian function and hormone signaling.5
• Inflammation: A leaky or inflamed gut can trigger systemic inflammation throughout the body. This inflammation puts stress on your adrenal glands, impacting cortisol production. This, in turn, can disrupt your progesterone and estrogen balance. Chronic inflammation can also exacerbate symptoms like period pain and contribute to conditions like polycystic ovarian syndrome (PCOS).

The Roadmap to Improving Gut Health for Hormonal Balance

I recommend the following active strategies to support your gut health for hormonal balance.

1. Start With a Gut Microbiome Test

Many patients tell me at their initial consultation that they’ve tried all sorts of supplements, diets, and other health tips to improve their gut health symptoms. If they noticed any improvements, the benefits were often short-lived, and their symptoms returned with a vengeance.

One of the main reasons for a lack of improvement or relapse in symptoms is that many people center their supplements and/or diet on guesses.

That’s why I’m a firm believer in a “test, don’t guess” approach.

All of my new patients start with a gut microbiome test to get an accurate picture of the state of your gut, allowing us to identify factors like:

• Dysbiotic bacteria or yeast that drive inflammation
• Levels of beneficial bacteria species

We can also test for leaky gut, food sensitivities, and low stomach acid production, all of which can contribute to systemic inflammation, gut issues, and pain.

2. Heal Leaky Gut

Once we have a clear picture, we take steps to support optimal gut function:

• Remove: Eliminate all identified infections (parasites, yeast, harmful bacteria) and offending dietary agents (based on testing).
• Replace: Support digestion and absorption using gut-soothing herbs and digestive enzymes.
• Re-inoculate: Probiotics have been shown to modulate the gut-brain axis and influence hormone levels. We use targeted probiotics (after testing) and fermented foods to rebalance the gut microbiome.6
• Repair: Heal the gut lining and improve gut integrity. This can be done with specific gut healing/soothing herbs like slippery elm.
• Rebalance: Implement lifestyle strategies like stress management and a nourishing diet to support optimal digestion and hormonal health.

3. Prioritize Short-Chain Fatty Acid Production

A critical part of improving gut health is to focus on short-chain fatty acid (SCFA) production. SCFAs are carbohydrate fermentation products produced by specific bacteria in your gut.7 The three main SCFAs in your intestine – acetate, propionate, and butyrate – don’t just aid in digestion. They are powerful signaling molecules, serve as energy sources, and assume pivotal roles in various systems.8,9

Studies suggest that SCFAs offer a wide range of benefits, such as:10

• Reducing inflammation
• Supporting healthy weight
• Improving blood sugar balance
• Protecting liver health
• Supporting heart health
• Helping prevent certain cancers
• Supporting brain and nervous system function

Recently published research indicates that SCFAs—particularly butyrate—may play a role in regulating women’s reproductive health.11 Disruptions in SCFA production or the bacteria that produce them have been linked to increased risk for:

• Pregnancy complications
• PCOS
• Endometriosis>
• Gynecological cancer

Simply put, SCFAs may be your golden ticket to achieving gut health for hormone balance.

So how can you boost SCFA production? By using food as medicine. Specifically, I recommend:

Increasing and diversifying fiber consumption:

• Resistant starches: Like the name suggests, resistant starches resist digestion in the upper GI tract, which allows them to reach the colon mostly unchanged.12 Resistant starches are fermented by specific bacteria species that lead to an increase in SCFA production.13 Resistant starches can also help improve the integrity of the gut barrier.14 Examples of foods that are high in resistant starch include beans, legumes, unripe bananas, plantains, seeds, and nuts.
• Inulin-type fructans: Inulin-type fructans are a type of fermentable dietary fiber known to help improve gut functions thanks to their prebiotic effects.15,16 Studies show that they:
  • Promote beneficial bacteria species
  • Improve intestinal barrier function
  • Increase insulin sensitivity
  • May help increase SCFA production.17

Common sources of inulin-type fibers include wheat, onion, garlic, leek, chicory root, bananas, artichokes, and asparagus.

• Pectins: Pectins are another type of dietary fiber with a growing body of evidence supporting their beneficial effects on gut health. In one animal study, pectin supplementation restored the amount of SCFAs after they were decreased, demonstrating their ability to enhance gut health.18

Taking an omega-3 supplement or boosting your omega-3 intake:

Studies show that omega-3 polyunsaturated fatty acids help enrich beneficial bacteria and SCFA production.19

Taking targeted probiotics:

Fermented foods are great sources of probiotics. But if you have a hard time tolerating fermented foods, you can consider targeted strains of probiotics, such as Bifidobacterium and Lactobacillus species. In a recently published study, patients with irritable bowel syndrome who took probiotics showed increased SCFA levels, leading to significantly lower inflammation and improved intestinal permeability.20

4. Adopt Healthy Lifestyle Habits

I also encourage you to adopt supportive daily habits for lasting gut health. Specifically, I recommend:

• Mastering stress management: Chronic stress can increase leaky gut and impair digestive function because it wreaks havoc on cortisol, your primary stress hormone.21,22 Dedicated daily practices like meditation or yoga can help reduce the pro-inflammatory burden on your hormones.
• Prioritizing sleep: Poor sleep disrupts your hormonal balance, which is governed by your circadian rhythm. Aim for 7 to 9 hours of high-quality, uninterrupted sleep every night.
• Practicing mindful eating: Slow down and chew your food thoroughly. Try not to eat when you’re stressed or distracted. Learn how to read food labels and track your food so you can see if there are any changes you can make.

Build the Foundation for Lifelong Hormonal Balance

Optimal hormonal balance doesn’t happen passively—and it’s not something you want to guess at. It takes accuracy, intention, and tested strategies that actually work.

As a naturopathic physician specializing in hormone health, I help women simplify the path to healing by building a strong foundation—starting with the gut.

Have questions?
Schedule a complimentary 15-minute consultation to see if I might be able to help you.