Your Gut & Nervous System

Most doctors treating hormone imbalances focus exclusively on replacing what’s deficient. Low estrogen? Here’s your patch. Low progesterone? Take this pill. Thyroid sluggish? Start this medication.

What they’re missing could be sabotaging your results.

In our first article, Dr. Christian Jenski and I discussed the hormone hierarchy—how cortisol, insulin, and thyroid function must be optimized before addressing sex hormones. But there’s a critical layer we need to explore: the systems that determine whether your body can actually use the hormones you’re giving it.

As Dr. Jenski explained in our recent conversation: “Optimization is how that hormone is being utilized, processed, metabolized by the body. Things like the gut are involved. Things like the influence of these endocrine loops are involved. The autonomic nervous system or neurologic system in general is involved.”

Today we’re diving into two overlooked systems that may explain why your hormone therapy isn’t working—or why you’re experiencing symptoms despite “normal” lab results.

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The Estrobolome: Your Gut’s Hormone Recycling Center

Here’s something that might surprise you: your gut contains a specialized community of bacteria whose sole job is managing estrogen metabolism. We call this the estrobolome.

When your liver processes estrogen through detoxification, it packages the hormone for elimination and sends it to your intestines. What happens next depends entirely on your gut microbiome.

The Beta-Glucuronidase Problem

In a healthy gut, estrogen metabolites get eliminated in your stool. But when your microbiome is imbalanced—a condition called dysbiosis—something problematic occurs.

Dr. Jenski described it perfectly: “There’s a complete branch of the microbiome called the estrobolome which is designed to help get rid of estrogen metabolites that have been detoxified. We often see on stool tests estrogen being recycled—the part that’s been neutralized is cleaved off, and we see it recycled back through the liver to be done twice.”

This recycling happens through an enzyme called beta-glucuronidase. When levels are elevated, your body reactivates estrogen that should have been eliminated, sending it back through your liver for another round of processing.

The result? Estrogen dominance symptoms despite normal or even low estrogen levels:

• Heavy, painful periods
• Breast tenderness
• Mood swings and irritability
• Weight gain (especially around hips and thighs)
• Fibrocystic breasts
• Increased cancer risk

As I’ve witnessed countless times in my practice: “I’ve had patients come in for hormone issues. We do the stool test on the first or second visit, and their beta-glucuronidase is sky high. They have elevated inflammatory markers and fat malabsorption issues. Just fixing those few things—they feel better. The cycles improve, acne clears up.”

For women with PCOS, perimenopause, or any hormone imbalance, addressing gut health isn’t optional—it’s foundational. Our articles on PCOS in Young Women and Hormones After 40 explore this connection in depth.

Supporting Your Estrobolome

To optimize estrogen metabolism through your gut:

Increase Fiber Intake

• Fiber binds to estrogen in your intestines, preventing reabsorption. Aim for 35–40 grams daily from:
• Cruciferous vegetables (broccoli, cauliflower, Brussels sprouts)
• Ground flaxseed (1–2 tablespoons daily)
• Legumes and beans
• Whole grains (if tolerated)

Add Fermented Foods
These provide beneficial bacteria that support healthy estrogen metabolism:

• Sauerkraut (raw, unpasteurized)
• Kimchi
• Kefir (if dairy-tolerant)
• Kombucha

Include Phytoestrogens
Plant compounds that help balance estrogen receptors:

• Ground flaxseed
• Sesame seeds
• Legumes
• Moderate amounts of organic soy (if appropriate)

Support Regular Bowel Movements
Aim for 1–2 well-formed bowel movements daily. Constipation allows more time for estrogen reabsorption.

For more detailed guidance on foods that support estrogen metabolism, see our Estrogen: The Younger Sister article.

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The Gut-Hormone Inflammation Loop

Beyond the estrobolome, gut dysfunction creates systemic inflammation that disrupts hormone balance throughout your body.

When your gut lining becomes permeable (often called “leaky gut”), bacterial fragments and undigested food particles enter your bloodstream. Your immune system treats these as threats, triggering chronic inflammation that:

• Increases insulin resistance (driving PCOS and weight gain)
• Disrupts thyroid hormone conversion
• Elevates cortisol (perpetuating the stress response)
• Interferes with hormone receptor sensitivity

The inflammation also affects how efficiently your body produces hormones. As discussed in our article: Progesterone: The Elder Sister, optimal progesterone synthesis requires adequate vitamin A, B6, C, and zinc—nutrients that become depleted when chronic inflammation is present.

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COMT: The Genetic Wild Card

Dr. Jenski brought up a crucial genetic factor that many practitioners overlook: COMT polymorphisms.

COMT (Catechol-O-Methyltransferase) is an enzyme that breaks down both stress hormones and estrogen. Some people have genetic variations—what Dr. Jenski calls “typos”—that slow this process down.

“If you have a COMT SNP or typo,” Dr. Jenski explained, “what’s happening is these catecholamines aren’t being broken down. You stay worked up, you can’t decompress. It’s the ‘worried warrior’ mentality where you stay in that revved-up state.”

This has profound implications:

For Stress Hormones:
People with COMT variations can’t efficiently clear adrenaline and noradrenaline. They remain in sympathetic overdrive—anxious, wired, unable to truly relax. This chronic stress elevates cortisol and disrupts the entire hormone hierarchy.

For Estrogen:
COMT is also how your body methylates estrogen metabolites for safe elimination. With sluggish COMT activity, estrogen metabolites—particularly the problematic 4-hydroxy pathway—accumulate.

As Dr. Jenski noted: “The COMT gene is also how we methylate estrogen as a byproduct. If you have a COMT SNP, that methylation is not happening well. Unfortunately, preferentially the 2-hydroxy becomes methylated. So you make the 4-hydroxy, it stockpiles, it’s not being neutralized… it becomes a problem.”

This is why the Hormones After 40 article emphasizes comprehensive hormone metabolite testing—to see not just your hormone levels, but how effectively you’re clearing them.

Supporting COMT Function:

• Magnesium (crucial cofactor for COMT)
• B vitamins (especially methylated forms for those with MTHFR variations)
• Glutathione or its precursors (NAC)
• Avoiding excessive methylation support (counterintuitively, some people with COMT issues become methyl-sensitive)

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The Autonomic Nervous System: The Fourth Pillar

During our conversation, I had a significant realization: “Maybe we need to add a fourth system—the autonomic nervous system—because how many of our patients with hormone difficulties don’t also have dysfunction in the nervous system?”

Dr. Jenski agreed immediately: “A hundred percent. How many dysautonomia patients do you have that don’t also have some hormone problems? They all have hormone problems.”

Understanding Sympathetic Dominance

Your autonomic nervous system has two branches:

Sympathetic (Fight-or-Flight):
Designed for short-term stress response. When activated chronically, it:

• Elevates cortisol and catecholamines
• Reduces digestive function (creating gut dysfunction)
• Impairs insulin sensitivity
• Disrupts ovulation and menstrual cycles
• Suppresses thyroid function

Parasympathetic (Rest-and-Digest):
Required for healing, hormone production, and detoxification. When suppressed, your body can’t:
Produce hormones efficiently

• Digest and absorb nutrients properly
• Eliminate toxins effectively
• Repair damaged tissues

As I explained to Dr. Jenski: “When someone’s in sympathetic overdrive (they have trauma)… those are the people who do really poorly when I start messing with the hormones if I have not addressed that stuff first.”

The Dysautonomia-Hormone Connection

Conditions like POTS (Postural Orthostatic Tachycardia Syndrome), mast cell activation syndrome, and connective tissue disorders often overlap with hormone imbalances.

The connection isn’t coincidental. As we discussed, chronic stress and trauma literally rewire your nervous system, keeping you stuck in fight-or-flight mode. This autonomic dysfunction then disrupts every hormone system.

Our Cortisol: The King of All Hormones article explores how HPA-axis dysfunction affects hormone production. The Progesterone article demonstrates how low progesterone manifests as anxiety and sleep disturbances—symptoms that worsen autonomic dysfunction.

Supporting Your Autonomic Nervous System

Vagal Nerve Stimulation:

• Deep, slow breathing (4-7-8 breath: inhale 4 counts, hold 7, exhale 8)
• Humming or gargling
• Cold water face immersion
• Gentle neck stretches

Meditation and Mindfulness:
Even 10 minutes daily measurably shifts nervous system balance.

Somatic Therapies:
For those with trauma history:

• EMDR (Eye Movement Desensitization and Reprocessing)
• Somatic Experiencing
• Internal Family Systems therapy

Movement:
Gentle, restorative exercise like tai chi, or walking in nature activates parasympathetic tone without triggering sympathetic overdrive.

Sleep Optimization:
Consistent sleep-wake times and adequate duration (7–9 hours) are non-negotiable for autonomic balance.

The Thyroid article notes how stress and nutrient deficiencies suppress thyroid function—another example of autonomic-hormone interconnection.

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Environmental Toxins: The Silent Disruptors

We can’t discuss gut health and hormone balance without addressing environmental toxin exposure.

Dr. Jenski emphasized a sobering statistic: “They did a study showing 40% of women with PCOS had detectable BPA levels. Almost half of women in this study with PCOS had detectable levels of BPA.”

BPA (Bisphenol A) has been “outlawed,” but as Dr. Jenski noted, it’s simply been “replaced by BPS, which will be outlawed and replaced by BPZ or whatever.”

These endocrine-disrupting chemicals don’t just affect you—they affect you transgenerationally. “They got into grandma, who got into your mom, who got into your eggs,” Dr. Jenski explained. “They’re gonna affect your offspring.”

The Most Common Hormone Disruptors

From our discussion and clinical experience:

Plastics (BPA, BPS, phthalates):

• Food storage containers
• Water bottles
• Canned food linings
• Receipt paper

Pesticides and Herbicides:

• Non-organic produce
• Lawn treatments
• Agricultural runoff in water

Personal Care Products:

• Parabens in cosmetics
• Triclosan in antibacterial products
• Fragrance chemicals (phthalates)

PFOAs (“Forever Chemicals”):

• Non-stick cookware
• Water-resistant clothing
• Stain-resistant furniture

As I shared from my research: “Right now the average American has 10–13 toxic chemicals in urine testing. Ten years ago it was only 6–8. Ten years before that it was 3–5.”

Our Our Silent Crisis article explores how environmental toxins are driving declining testosterone and fertility issues, while the CIRS vs Hypothyroid post discusses mold and biotoxin-related hormone disruption.

Practical Detoxification Strategies

Replace Plastic with Glass or Stainless Steel:
Food storage, water bottles, and cookware.

Filter Your Water:
Remove chlorine, fluoride, heavy metals, and pesticide residues.

Choose Organic (Strategically):
Use the Environmental Working Group’s “Dirty Dozen” list to prioritize which produce to buy organic.

Purify Indoor Air:
HEPA filters remove particulates; houseplants and proper ventilation reduce toxin accumulation.

Use Clean Personal Care Products:
The EWG Skin Deep database rates product safety.

Support Liver Detoxification:
Cruciferous vegetables, citrus, herbs, adequate hydration, and regular bowel movements.

Sweat Regularly:
Exercise and sauna therapy help eliminate fat-soluble toxins.

The Estrogen article provides detailed guidance on foods that support estrogen clearance and detoxification.

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Nutrient Deficiencies: The Foundation Failure

Here’s where many hormone optimization efforts fail: you can’t run sophisticated biochemical processes without the raw materials.

As I emphasized to Dr. Jenski: “How are hormones gonna work without magnesium and calcium being balanced?”

He agreed: “Insulin receptors don’t work without magnesium. Thyroid receptors don’t work without vitamin D and A.”

Critical Nutrients for Hormone Function

Vitamin D:
Required for insulin receptor function and thyroid hormone utilization. Most Americans are deficient. Optimal levels: 60-80 ng/mL.

Magnesium:
Cofactor for over 300 enzymatic reactions, including hormone synthesis and receptor function. Deficiency is epidemic (affecting ~50% of Americans).

B Vitamins:
Especially important for:

• Methylation (B12, folate, B6)
• Stress hormone production (B5)
• Neurotransmitter synthesis (B6)
• Energy production (B1, B2, B3)

Iodine and Selenium:
Essential for thyroid hormone production. Many following “clean” diets inadvertently become deficient.

Zinc:
Required for progesterone production, testosterone synthesis, and immune function.

Tyrosine:
Amino acid precursor for thyroid hormones and catecholamines.

Thiamine (B1):
Dr. Jenski emphasized this often-overlooked nutrient’s role in autonomic dysfunction. Deficiency can cause symptoms mimicking dysautonomia.

I also noted an observation about hypermobile patients (roughly 20% of the population): “If you’re hypermobile, you’re gonna have a tendency towards deficiencies in a lot of amino acids, vitamin C, trace minerals, and you tend to have low vitamin D levels.”

The Progesterone article lists specific nutrients required for progesterone synthesis, while the Thyroid article covers minerals critical for thyroid function.

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The Auto-Correction Phenomenon

One of the most gratifying aspects of addressing these underlying systems is what Dr. Jenski calls “auto-correction.”

As he explained: “Do you not see, as you’re working on one thing, three other things get better? That’s not a coincidence. It’s just how the system works.”

I see this constantly: “For young women, we fix the hormones by fixing gut health, stress, and environment. Suddenly cycles normalize, acne clears, energy returns.”

This is why we emphasize foundational work before hormone replacement. Often, once you optimize:

• Gut function and microbiome
• Stress response and autonomic balance
• Sleep quality and circadian rhythm
• Nutrient status
• Environmental toxin exposure

The body’s natural hormone production and utilization improve dramatically—sometimes eliminating the need for hormone replacement entirely.

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The Bigger Picture

As Dr. Jenski summarized beautifully: “The body just does that. The body just auto-corrects. The whole goal is education—not just to repair and fix someone. They’re not broken. They don’t need to be fixed. They just need to be taught how to live, how to be healthy.”

Your gut and nervous system aren’t separate from your hormone health—they’re integral to it. Addressing these systems isn’t a detour from hormone optimization; it’s the foundation that makes optimization possible.

In our next article, we’ll translate all of this into practical testing strategies. We’ll discuss which labs to order, when to use serum versus saliva versus urine testing, and how to interpret results in the context of your unique situation.

Read Next: Testing & Tracking: How to Measure What Matters (Coming Soon)

Continue exploring hormone optimization:

• Cortisol: The King of All Hormones
• Insulin: Our Sticky Problem
• Thyroid: The Conductor
• PCOS in Young Women
• Hormones After 40
• CIRS vs Hypothyroid

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This is the second article in a four-part series based on conversations between Dr. Aaron Hartman and Dr. Christian Jenski about hormone optimization. The information provided is for educational purposes and should not replace personalized medical advice from your healthcare provider.