The Estrobolome: How Your Gut Influences Menopause and Your Thyroid

In this article

As you move through perimenopause and menopause, it can feel like your body flips a switch overnight—cue the hot flashes, wild mood swings, restless nights, relentless fatigue, and that stubborn belly fat that just won’t budge. While shifting hormones usually take the blame, a hidden powerhouse in your body deserves way more attention: your gut.

More specifically, meet the estrobolome—a specialized group of gut bacteria that helps regulate estrogen levels. Emerging research reveals that the health of your estrobolome could dramatically influence how you navigate midlife. We’re talking everything from how much weight you gain (and where it lands), to your emotional well-being, and even your long-term risk of chronic illness.

Are you curious what the estrobolome actually is, how it works, and what it has to do with your thyroid? More importantly, do you want to know how to support it to feel better, balance your hormones naturally, and reclaim your energy and mood? Read on to discover the gut-hormone connection that could change your midlife health journey.

The estrobolome is a subset of the gut microbiome, specifically, the collection of bacteria in your intestines capable of metabolizing estrogen. During perimenopause and menopause, declining ovarian estrogen production shifts reliance to the estrobolome to maintain your hormonal balance.

The bacteria in your estrobolome produce enzymes, primarily beta-glucuronidase, which reactivates estrogen by converting it from its conjugated (inactive) form to its free (active) form. This process determines how much estrogen circulates in your bloodstream, versus being excreted through your digestive system.

In a healthy estrobolome, estrogen is metabolized and balanced efficiently. But when the estrobolome is disrupted—a condition known as dysbiosis—this balance is thrown off. A dysregulated estrobolome can exaggerate the hormonal shifts of perimenopause and menopause, making symptoms worse.

Too much estrogen can be reabsorbed, leading to estrogen dominance. And low estrogen circulation can worsen estrogen deficiency and menopausal symptoms, including: 

• More intense hot flashes
• Increased mood swings and anxiety
• More fatigue
• Greater belly fat accumulation
• Heightened risk of osteoporosis and cardiovascular disease

And this isn’t just a hormonal story. Your estrobolome and broader gut microbiome influence inflammation, metabolism, immunity, and brain function, all critical during midlife and beyond

It’s not just that your gut affects your hormones; your hormones also affect your gut.

Drops in estrogen and progesterone directly impact your gut microbiome composition35. Estrogen protects the gut lining and helps maintain a diverse and healthy microbiome. As estrogen declines in perimenopause and menopause, many women experience:

Increased gut permeability (“leaky gut”) -- Estrogen plays a key role in maintaining the integrity of the gut lining by supporting tight junctions between intestinal cells. When estrogen levels drop, these junctions can loosen, allowing unwanted substances like toxins, pathogens, and undigested food particles to pass into the bloodstream. This contributes to systemic inflammation, which may worsen hormonal imbalances and increase the risk for autoimmune conditions and food sensitivities.

Reduced diversity – Postmenopausal women often exhibit a decline in gut microbial diversity—the range of beneficial bacteria residing in the gut. A diverse microbiome is essential for regulating inflammation, supporting digestion, and balancing metabolism. Lower diversity has been linked to insulin resistance, increased fat storage, and higher levels of inflammatory markers, all of which are common concerns during and after menopause.

“Masculinization” of the microbiome – After menopause, the gut microbiome begins to resemble that of men more closely. This shift is characterized by an increase in bacteria like Bacteroides and Prevotella, which are associated with a higher risk of obesity and chronic inflammation, and a decrease in Firmicutes, a group of bacteria involved in fermenting fiber into short-chain fatty acids that nourish the gut lining. These changes may contribute to weight gain, reduced nutrient absorption, and metabolic disturbances commonly seen in menopausal women.

Slower gut motility –  Estrogen and progesterone help regulate the smooth muscle contractions that move food through the digestive tract. When these hormone levels fall, gut motility can slow down. This can lead to a sluggish digestive process, making women more prone to bloating, gas, and a feeling of fullness even after small meals.

Increased constipation or bloating – With slower transit times and reduced gut muscle tone, constipation becomes more common. Estrogen also influences bile production, which helps digest fats and maintain regular bowel movements. Declines in bile flow, combined with a slower-moving gut, can lead to uncomfortable bloating, abdominal discomfort, and irregular bowel habits, further disrupting microbiome balance.

This creates a vicious cycle. Lower estrogen levels weaken gut health and the estrobolome’s ability to maintain hormonal balance, which in turn worsens estrogen imbalance. Supporting both hormonal and gut health becomes critical in breaking this cycle and promoting overall well-being during perimenopause and menopause.

One of the most frustrating symptoms of menopause is weight gain, especially around the belly. Estrogen plays a key role in regulating where fat is stored. When estrogen drops, women tend to accumulate visceral fat—the deep abdominal fat linked to insulin resistance, inflammation, and chronic disease.

But the gut—specifically the estrobolome—can amplify this issue in several ways:

Gut dysbiosis during perimenopause and menopause contributes to abdominal weight gain through:

• Increased estrogen imbalance – A dysbiotic estrobolome can either cause excess estrogen (worsening symptoms like water retention, mood swings, and weight gain) or estrogen deficiency (exacerbating belly fat accumulation and metabolic slowdown).
• Higher inflammation – Pathogenic bacteria release lipopolysaccharides (LPS) – An unhealthy gut produces inflammatory compounds like lipopolysaccharides (LPS), which trigger inflammation, worsen insulin resistance, and promote fat storage, particularly in the abdominal area.
• Slower metabolism – Chronic inflammation and hormonal imbalance can lead to dysbiosis, which reduces short-chain fatty acid (SCFA) production, impairing fat oxidation and insulin sensitivity. Your metabolic rate can drop, making it harder to burn calories efficiently.
• Blood sugar imbalance – Gut dysbiosis can also interfere with insulin signaling and blood sugar control, leading to cravings, energy crashes, and weight gain.

‍

THYROID GUIDE

How To Maintain A Healthy Gut

Digestive issues like bloating, constipation, or gas can be resolved or improved with simple lifestyle changes

Thank you! Check your mailbox for your guide

Oops! Something went wrong while submitting the form.

‍

The estrobolome also plays a significant role in hypothyroidism and Hashimoto’s thyroiditis. Disruptions in the estrobolome can alter estrogen balance, impact thyroid hormone availability, and increase autoimmune activity, potentially worsening hypothyroid symptoms and Hashimoto’s progression. Recognizing this gut-thyroid connection highlights the importance of gut health in managing thyroid disorders.

Estrogen, autoimmunity, and the immune response

Estrogen has a complex relationship with immunity. In some cases, high estrogen levels may worsen autoimmune disease activity, particularly in genetically susceptible individuals (like those with Hashimoto’s). If the estrobolome is recirculating estrogen excessively due to imbalances in beta-glucuronidase activity, it can:

• Fuel autoimmune inflammation

• Trigger flares in Hashimoto’s

• Contribute to fatigue, brain fog, and mood issues typical of both conditions

The estrobolome and autoimmune Hashimoto’s

The estrobolome is part of the broader gut microbiome, which helps:

• Maintain the integrity of the gut lining (to prevent leaky gut)

• Train and balance the immune system

• Regulate systemic inflammation

An unhealthy estrobolome may both initiate and perpetuate Hashimoto’s by promoting gut dysfunction and immune imbalance in several ways.

• Leaky gut (intestinal permeability) – Dysbiosis compromises intestinal barrier integrity, allowing bacterial toxins to enter your circulation, allowing food particles and toxins to escape into the bloodstream, triggering autoimmune flares.

• Molecular mimicry – immune responses cross-react with bacterial proteins that resemble thyroid proteins, confusing the immune system and worsening Hashimoto’s attacks.

• Inflammasome activation –  Gut pathogens like Bacteroides and Prevotella (often reduced in Hashimoto’s patients) promote NLRP3 inflammasome activity, driving autoimmune thyroid destruction.

• Reduced regulatory T cells (Tregs) – A healthy microbiome supports Tregs, which dampen autoimmune responses. Dysbiosis shifts the balance toward pro-inflammatory Th17 cells, worsening thyroid autoimmunity.

Estrobolome dysfunction, estrogen imbalance, and your thyroid

An imbalanced estrobolome can lead to estrogen dominance, and excess estrogen has several effects on the thyroid. Excess estrogen:

• Inhibits the conversion of thyroid hormone T4 to active T3.

• Increases levels of thyroxine-binding globulin (TBG), which reduces free triiodothyronine (free T3) and free thyroxine (free T4), the active forms of thyroid hormone, leading to hypothyroid symptoms, even if total hormone levels appear normal.

• Promotes autoimmune reactivity by upregulating thyroid peroxidase (TPO) antibodies, a hallmark of Hashimoto’s.

Conversely, low estrogen levels (e.g., during menopause) may also affect thyroid hormone receptor sensitivity and conversion of T4 to T3.

Gut-thyroid axis in hypothyroidism

Your gut health directly impacts your thyroid function through several mechanisms:

• Gut motility – Hypothyroidism slows gut motility, increasing constipation and dysbiosis. Since estrogen metabolism relies on regular bowel movements and microbial balance, sluggish digestion caused by hypothyroidism worsens estrobolome dysfunction, creating a vicious cycle.
• Nutrient absorption – The gut absorbs iodine, selenium, zinc, and iron, which are critical for thyroid hormone synthesis. Dysbiosis (gut imbalance) can cause deficiencies, impairing thyroid hormone production.
• T4-to-T3 conversion – Up to 20% of T4 is converted to active T3 in the gut via microbial enzymes. Dysbiosis reduces this conversion, worsening hypothyroidism.
• Immune modulation – 80% of the immune system resides in the gut. Dysbiosis triggers systemic inflammation, which may suppress thyroid function.

‍

Are you wondering if your gut is contributing to your perimenopausal or menopausal symptoms? Here are some clues your estrobolome may be out of sync:

• Frequent bloating, gas, or constipation: Imbalanced gut flora can slow digestion and impair estrogen elimination, leading to gastrointestinal discomfort.
• Increased food sensitivities or intolerances: A disrupted gut barrier can trigger immune responses to certain foods, especially those high in histamine or gluten.
• Chronic fatigue: Poor estrogen detox and gut dysbiosis can impair mitochondrial function and nutrient absorption, contributing to low energy.
• More intense PMS or perimenopausal symptoms: Symptoms like breast tenderness, mood swings, and cramping around and during your menstrual cycles may worsen due to unbalanced estrogen levels or estrogen dominance.
• Worsening hot flashes or night sweats: Dysbiosis disrupts serotonin production (90% of which occurs in the gut), affecting temperature regulation. This can intensify vasomotor symptoms like hot flashes and night sweats.
• Weight gain, especially around the belly and waist: Estrogen imbalance and inflammation can promote fat storage, particularly in the abdominal region.
• Insulin resistance or blood sugar imbalances: Gut dysbiosis and estrogen dysregulation can impair insulin sensitivity, increasing the risk of prediabetes or type 2 diabetes.
• History of frequent antibiotic use or chronic stress: Antibiotics can wipe out beneficial gut bacteria, while stress increases cortisol, both disrupting the estrobolome.
• Gastrointestinal disorders: Irritable bowel syndrome (IBS), small intestinal bacterial overgrowth (SIBO), and leaky gut often coexist with an imbalanced estrobolome and can interfere with estrogen metabolism.
• Mood imbalances: Estrogen plays a key role in brain chemistry; imbalances may contribute to mood instability, irritability, or low mood. Gut bacteria produce GABA and dopamine. Dysbiosis skews production toward stress hormones like cortisol.
• Unexplained mood swings or irritability: Estrogen fluctuations—amplified by poor gut health—can affect neurotransmitter levels, leading to emotional instability.
• Heavy or irregular periods: Estrogen dominance due to poor detoxification can cause a thickened uterine lining and heavier menstrual bleeding.
• Breast tenderness or fibrocystic breasts: Another sign of excessive or poorly metabolized estrogen recirculating in the body.
• Brain fog or difficulty concentrating: Estrogen influences cognitive clarity; imbalance can contribute to cognitive sluggishness, especially in midlife women.
• Skin issues like acne, rosacea, or rashes: A sluggish estrobolome can lead to hormonal skin flare-ups or inflammation-related skin issues.
• Low libido: Estrogen dysregulation and gut inflammation can suppress sexual desire and hormone balance.

While standard stool tests don’t typically assess the estrobolome specifically, comprehensive gut tests (like GI-MAP or Genova’s GI Effects) can give insight into:

• Microbiome diversity

• beta activity

• Presence of pathogens or dysbiosis

Functional medicine providers can interpret these results and tailor a plan based on your individual gut profile.

Fortunately, your estrobolome is modifiable. With the right strategies, you can nurture your gut, improve estrogen metabolism, and reduce many frustrating menopausal symptoms. And there’s an extra benefit: these approaches are all supportive of better health for hypothyroidism and Hashimoto’s patients. :

Eat more fiber (especially prebiotic fiber)

Dietary fiber feeds your gut bacteria and helps estrogen be appropriately excreted. A fiber-rich diet can also help stabilize serotonin levels.

Experts recommend that you focus on:

• Flaxseeds (contain lignans that bind excess estrogen)

• Chicory root, onions, garlic, leeks, artichokes, asparagus

• Oats, apples, and legumes (like lentils)

Eat foods rich in polyphenols

Eating more polyphenol-rich foods can significantly support the health of your estrobolome. Polyphenols – natural compounds found in plant-based foods –  act as prebiotics by feeding beneficial gut microbes that help maintain hormonal balance. Polyphenols also help regulate the enzyme beta-glucuronidase. In addition to supporting hormone balance, polyphenols have powerful anti-inflammatory and antioxidant properties that protect the gut lining and reduce inflammation, which is essential for a well-functioning estrobolome.

Polyphenol-rich foods to include in your diet include:

• Berries (blueberries, blackberries, raspberries, strawberries)
• Apples (especially with the peel)
• Red grapes and red wine (in moderation)
• Dark chocolate (70% cacao or higher)
• Green tea and black tea
• Extra virgin olive oil
• Red onions
• Flaxseeds
• Walnuts
• Turmeric
• Rosemary, thyme, and oregano
• Artichokes
• Spinach
• Broccoli

Add fermented foods

Fermented foods help diversify your microbiome and support estrogen metabolism. Include:

• Yogurt (unsweetened)

• Kefir

• Kimchi

• Kombucha

• Sauerkraut

• Miso

• Tempeh

Start with small amounts daily and increase as tolerated.

Consider probiotic supplements

Certain probiotics may support estrogen balance and reduce belly fat, especially strains like:

• Lactobacillus acidophilus La-14

• Lactobacillus rhamnosus HN001

• Lactobacillus rhamnosus GG

• Bifidobacterium lactis

• Bifidobacterium breve

Look for multi-strain formulas with at least 10 billion CFUs. And remember that timing matters. Take probiotics before bed to enhance overnight gut repair

Reduce alcohol and sugar intake

Both sugar and alcohol disrupt the microbiome and increase estrogen recirculation. They also contribute to belly fat and blood sugar spikes. Try reducing or eliminating them for at least 30 days to see how your body responds.

Limit xenoestrogens and endocrine disruptors

Chemicals in plastics, pesticides, and personal care products can mimic estrogen and interfere with hormone metabolism. Avoid:

• BPA and phthalates (found in plastics and cans)

• Conventional beauty products (switch to EWG-verified brands)

• Non-organic produce (buy organic when possible)

Support liver function

Your liver plays a crucial role in estrogen detoxification. Support it with:

• Cruciferous vegetables (broccoli, kale, cabbage, Brussels sprouts)

• Bitter greens (dandelion, arugula)

• Lemon water

• Milk thistle (supplement)

• DIM

Stay physically active

Exercise helps regulate insulin, reduce inflammation, and support gut motility. Both resistance training and aerobic exercise are beneficial. Aim for:

• 150 minutes of moderate physical activity weekly

• 2–3 strength training sessions per week

Manage stress

Stress negatively impacts your gut through the gut-brain axis. Chronic cortisol release:

• Increases belly fat

• Disrupts sleep

• Alters microbiome composition

Practice stress management techniques like:

• Yoga

• Meditation

• Breathwork

• Spending time in nature

Breathwork is also especially helpful. Even 5 minutes of diaphragmatic breathing daily not only helps with stress management, but it also reduces gut permeability.

Sleep well

Poor sleep is linked to hormonal imbalance, gut dysbiosis, and weight gain. To support both gut and hormone health:

• Keep a consistent sleep schedule

• Avoid screens 1 hour before bed

• Use blackout curtains and a cool room

• Limit caffeine after noon

This is a somewhat complex question. While HRT, such as estrogen therapy, can provide symptom relief and long-term benefits for many women, its effectiveness—and how your body metabolizes it—can be impacted by your estrobolome.

If your gut is unhealthy, HRT may:

• Be less effective

• Increase side effects (e.g., bloating, mood changes)

• Worsen estrogen dominance symptoms

Ideally, work on your gut health first (or alongside starting HRT) for the best results. Think of your gut as the foundation—without a healthy estrobolome, hormone therapy might not work as intended.

Looking ahead, emerging research suggests personalized microbiome testing could soon guide hormone therapy and probiotic interventions. While science is still unraveling the gut-hormone link, evidence already underscores a powerful truth: nurturing your estrobolome may be the key to thriving – not just surviving – this transition.

Meanwhile, the estrobolome isn’t just a buzzword; it’s a lifeline! By addressing gut and hormonal health, you can:

• Ease the transition through perimenopause and menopause

• Reduce belly fat and inflammation

• Support natural hormone detoxification

• Improve mood, sleep, and energy

• Prevent long-term chronic disease

Paloma Health offers personalized, evidence-based care to help you feel your best—no matter where you are on your health journey. Whether you’re managing Hashimoto’s, struggling with hypothyroidism, navigating the hormonal shifts of perimenopause and menopause, or looking for sustainable weight loss solutions, Paloma Health provides expert medical support tailored to your unique needs. Paloma’s holistic approach also supports gut health and a balanced estrobolome, essential for hormonal harmony, especially during midlife transitions. Paloma combines cutting-edge testing, ongoing virtual care from expert providers, and lifestyle guidance to help you regain energy, balance your hormones, and enjoy lasting wellness and quality of life.

• The estrobolome is a group of gut bacteria that helps regulate estrogen metabolism, influencing symptoms during perimenopause and menopause.

• When imbalanced, the estrobolome can contribute to estrogen dominance or deficiency, worsening hot flashes, mood swings, fatigue, and belly fat.

• Declining estrogen levels weaken the gut barrier and reduce microbial diversity, fueling inflammation, insulin resistance, and digestive issues.

• Gut health and hormonal health are tightly linked, with dysbiosis creating a vicious cycle that worsens menopausal and thyroid symptoms.

• A dysfunctional estrobolome can impair thyroid hormone activation and promote autoimmunity, increasing the risk and severity of Hashimoto’s.

• Signs of estrobolome imbalance include bloating, brain fog, mood swings, skin issues, low libido, and irregular or heavy periods.

• Although standard tests don’t directly assess the estrobolome, comprehensive stool testing can provide clues for targeted gut support.

• Supporting gut health through a high-fiber diet, stress reduction, and probiotics can improve estrogen balance and relieve menopause and thyroid-related symptoms.