The Link Between SIBO and Your Thyroid

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Your thyroid and your gut are far more connected than you might think. When one is out of balance, the other often feels the impact—and this connection is vital for anyone with thyroid disorders, particularly autoimmune Hashimoto’s thyroiditis, the leading cause of hypothyroidism in the U.S. Inflammation, bacterial imbalances, thyroid dysfunction, and hormonal issues frequently go hand-in-hand, which is why small intestinal bacterial overgrowth, or SIBO, is surprisingly common among people with thyroid issues. For women navigating perimenopause and menopause, these gut-thyroid interactions can become even more pronounced, affecting digestion, metabolism, and overall hormonal balance. Let’s dive into the powerful link between SIBO, thyroid health, and how it intersects with autoimmunity, Hashimoto’s, and midlife hormonal shifts.

Small intestinal bacterial overgrowth, or SIBO, happens when too many bacteria—especially types not generally found in your small intestine —start growing. This part of your digestive system is where most of the food breakdown and nutrient absorption happens. When these bacteria multiply beyond normal levels, they interfere with digestion and absorption, causing uncomfortable symptoms.

SIBO often begins when something slows down the movement of food and waste through your small intestine. Think of it like a traffic jam in your gut—when things move too slowly, bacteria get a chance to overgrow. Medical conditions like diabetes, hypothyroidism, or structural changes from surgeries can cause this slowdown. When bacteria multiply in this overcrowded environment, they produce toxins and gases that upset your digestion and stop your body from absorbing essential nutrients.

This bacterial buildup causes a range of disruptive effects—from bloating and stomach pain to diarrhea and weight loss—as your gut struggles to function properly. The overgrowth also messes with bile acids, making fat digestion harder, and may even damage the lining of your intestines. Because SIBO impairs nutrient absorption, it can, over time, lead to deficiencies and malnutrition.

In short, SIBO is a mix of too many unwelcome bacteria and a sluggish gut environment that lets them take over. If you experience persistent digestive symptoms, especially with known risk factors, it’s important to talk to your doctor for an accurate diagnosis and treatment plan. Understanding how SIBO disrupts your gut helps you see why prompt care is key to restoring your digestive health.

Risk factors for SIBO primarily involve conditions that slow or disrupt the normal movement and clearance of bacteria in the small intestine, as well as structural changes and immune system impairments. These factors create an environment where bacteria can multiply excessively.

Key risk factors include:

• Impaired intestinal motility: Conditions like hypothyroidism, diabetes, scleroderma, and gastroparesis slow the passage of food and waste through the small intestine, allowing bacteria to overgrow.
• Structural abnormalities: Surgical procedures (such as gastric bypass or bowel resections), strictures, adhesions (scar tissue), diverticula (small pouches), and fistulas can cause trapping of bacteria.
• Reduced stomach acid or digestive secretions: Low stomach acid (hypochlorhydria), often from aging or proton pump inhibitor (PPI) use, reduces your natural bacterial control.
• Immune system deficiencies: Disorders such as AIDS, IgA deficiency, or other immunodeficiencies reduce the gut’s ability to regulate bacterial populations.
• Previous gastrointestinal surgery or radiation: These treatments can alter anatomy and motility, increasing your risk.
• Chronic diseases: Conditions such as Crohn’s disease, celiac disease, chronic pancreatitis, and liver cirrhosis are linked to a higher risk.
• Age: Older adults are more susceptible due to decreased acid production and motility.

Other contributing factors may include diets high in fermentable carbohydrates, which feed bacteria and promote overgrowth. Together, these risk factors disrupt the delicate balance of the gut and favor bacterial proliferation in the small intestine, leading to SIBO symptoms.

If any of these factors apply and symptoms are present, medical evaluation is advised for proper diagnosis and treatment.

SIBO can lead to a cluster of digestive and systemic symptoms. These symptoms can overlap with other gastrointestinal conditions, so proper diagnosis by a healthcare professional is crucial if you experience these signs.

Key digestive symptoms

• Loss of appetite is common and may be due to discomfort, bloating, or a feeling of fullness that discourages eating.
• Nausea can occur when bacteria disrupt normal digestion, sometimes accompanied by queasiness or an unsettled stomach.
• Bloating is reported by most SIBO patients, resulting from bacterial fermentation of carbohydrates and subsequent gas production, which can lead to a feeling of tightness or visible abdominal swelling. ​
• Abdominal pain tends to present as cramping, discomfort, or pressure, often after meals, due to intestinal gas and distension.

Changes in bowel habits

• Diarrhea is frequent and is often caused by poor absorption of fats and other nutrients, as bacteria break down bile salts needed for fat digestion. ​
• Some patients may experience constipation instead of, or alternating with, diarrhea due to changes in the gut environment and motility.
• Excessive gas—such as burping or flatulence—results from fermentation activity by the overgrown bacteria.

Nutrition and weight effects

• Unintentional weight loss can occur when chronic malabsorption prevents the body from retaining sufficient nutrients or calories.
• Malnutrition is a risk when the absorption of vitamins (such as B12 and D), minerals, fats, and carbohydrates is impaired by bacterial overgrowth.
• Feeling uncomfortably full after eating (early satiety) often results from distension and motility disturbances in the affected gut segment.

Additional and systemic symptoms

• Fatigue and weakness can result from chronic malabsorption and vitamin or mineral deficiencies, leading to reduced overall energy.
• Headaches, brain fog, and poor concentration have been reported in more severe or prolonged cases, likely stemming from nutritional deficits or gut-brain axis effects. ​

If you have persistent gastrointestinal symptoms—especially those listed above—it is essential to seek medical evaluation. Diagnosis often requires specialized breath testing or small bowel sampling to confirm the condition before treatment.

Testing for SIBO primarily involves either a breath test or a fluid culture obtained during an endoscopy, with the breath test preferred for most due to its non-invasive nature and convenience.

The breath test works by detecting specific gases—hydrogen and methane—that bacteria produce when they ferment carbohydrates in your small intestine. During the test, you drink a sugar solution, commonly glucose or lactulose mixed with water, which serves as fuel for the bacteria. Over the next 2 to 3 hours, you breathe into a special device at regular intervals, which measures the levels of these gases in your exhaled breath. A rapid rise in hydrogen or methane gas indicates possible bacterial overgrowth. Proper preparation is crucial: patients typically avoid certain medications (such as antibiotics, probiotics, antacids, and laxatives) and follow a specific diet in the days leading up to the test to ensure accurate results. The test is safe and generally well-tolerated with no restrictions afterward.

Endoscopic fluid aspiration is considered the gold standard for diagnosis, despite being invasive. During this procedure, a physician uses an endoscope to collect fluid directly from the small intestine, which is then cultured to precisely identify bacterial overgrowth. However, this method is less commonly used due to its invasiveness, cost, and accessibility limitations.

Alongside these tests, doctors may order blood tests to assess vitamin and mineral levels, since SIBO can cause malabsorption, and stool tests to evaluate fat malabsorption or exclude other infections. Combining these diagnostic tools helps form a comprehensive understanding of the condition and guides appropriate treatment decisions. ​

Overall, the breath test remains the widely used, practical approach for diagnosing SIBO, while endoscopy with fluid culture offers definitive confirmation when necessary.

Treating SIBO requires a comprehensive, personalized approach that not only aims to reduce excessive bacterial populations in the small intestine but also addresses the underlying causes and helps restore healthy gut function. Because SIBO often results from a complex interplay of impaired gut motility, structural issues, dietary factors, and, at times, other health conditions, effective treatment involves multiple components working together.

Correcting the underlying problem

The foundational step in SIBO treatment is identifying and correcting any underlying medical problems that contribute to bacterial overgrowth. For example, if a person develops SIBO as a complication of delayed gastric emptying after gastric surgery, surgical revision, or specific gastrointestinal therapies may be necessary to restore normal motility and prevent recurrence. Similarly, individuals with hypothyroidism need proper management of their thyroid hormone levels and a regimen that supports regular bowel movements, as low thyroid function can cause slow gut motility that favors bacterial overgrowth. Addressing these root causes is essential to prevent SIBO from returning after treatment.

Antibiotics for bacterial reduction

Antibiotics are the most commonly prescribed treatment for SIBO. They work by temporarily reducing excess bacteria in the small intestine, helping relieve symptoms such as bloating, diarrhea, and abdominal pain. Rifaximin is the preferred antibiotic due to its minimal absorption into the bloodstream and targeted action within the gut, resulting in fewer systemic side effects. In cases where methane-producing bacteria dominate, a combination of rifaximin and neomycin may be used to target different bacterial populations effectively.

However, antibiotics have limitations. They can also wipe out beneficial bacteria, sometimes causing symptoms similar to SIBO, such as diarrhea or discomfort. Because of the risk of relapse, some patients require multiple courses or adjunct therapies. Medical practitioners often tailor antibiotic regimens based on breath test results, indicating which gases—hydrogen or methane—are predominant in the gut. ​

Probiotics to restore healthy bacteria

Probiotics—supplements containing live beneficial bacteria—can be a valuable part of treatment, mainly when used alongside antibiotics. They help restore the balance of gut microbiota by replenishing good bacteria that may be depleted during antibiotic therapy. Probiotics may also help improve gut barrier integrity, reduce inflammation, and support digestive health.

The choice of probiotic strains, timing, and dosage matters. Some evidence suggests that certain probiotics can help reduce SIBO symptoms and prevent relapse, but more research is needed to identify the most effective strains for different types of SIBO.

Dietary modifications to starve bacteria

Diet plays a crucial role in managing SIBO because specific carbohydrates—especially fermentable sugars—feed the overgrown bacteria, worsening symptoms. Reducing or eliminating these carbohydrates starves the bacteria, reducing fermentation and gas production.

Common dietary strategies include:

• Low-FODMAP diet: Avoids fermentable oligosaccharides, disaccharides, monosaccharides, and polyols, which are types of carbohydrates that are poorly absorbed and highly fermentable by bacteria. This diet is often followed for several weeks to calm symptoms before gradually reintroducing foods.
• Elemental diet: A liquid formula made up of easily absorbed nutrients designed to “starve” the bacteria while nourishing the patient. It’s generally used for severe or refractory SIBO cases.
• Specific Carbohydrate Diet (SCD) and GAPS diet: These restrict complex carbohydrates and grains to reduce bacterial fermentable sources.

These diets require guidance and monitoring because overly restrictive eating can lead to nutrient deficiencies and affect quality of life. ​

Supplements to prevent deficiencies

Since SIBO impairs nutrient absorption, vitamin and mineral supplementation is often necessary. Common deficiencies include vitamin B12, iron, calcium, vitamin D, and magnesium, which can contribute to fatigue, bone loss, and other systemic symptoms.

Some patients need vitamin B12 injections if oral absorption is severely impaired by bacterial overgrowth. Supplementation helps correct malnutrition, supports overall health, and improves recovery during and after SIBO treatment. ​

Motility support and lifestyle changes

Supporting normal gut motility is crucial for long-term SIBO management. Prokinetic agents—medications or natural supplements that enhance intestinal muscle contractions—are often recommended, especially after antibiotic courses. This helps maintain the gut’s natural ability to “flush” bacteria and prevent recurrence.

Lifestyle measures such as regular physical activity, stress reduction, staying well hydrated, and eating smaller, more frequent meals also support motility and gut health. Avoiding medications like chronic proton pump inhibitors unless necessary reduces the risk of creating an environment that favors bacterial overgrowth and promotes bloating.

Follow-up and prevention of relapse

SIBO has a relatively high relapse rate, so follow-up care is an integral part of treatment. After antibiotics or antimicrobials complete their course, patients often undergo symptom reassessment and, in some cases, repeat breath testing. Maintenance strategies, including diet adjustments, probiotics, and motility management, are tailored to each individual.

Screening for and treating underlying conditions such as diabetes, thyroid disorders, or anatomical abnormalities are equally important in preventing recurrence.

SIBO and thyroid health—especially autoimmune thyroid diseases like Hashimoto’s thyroiditis—are closely linked through multiple complex mechanisms involving gut motility, immune system regulation, inflammation, and nutrient absorption. Understanding their interaction sheds light on why people with thyroid conditions are at higher risk of developing SIBO, while SIBO itself may exacerbate or even trigger autoimmune thyroid dysfunction.

How SIBO and thyroid function interact

The small intestine normally contains relatively few bacteria compared to the colon. However, in SIBO, bacteria that typically inhabit the large intestine grow excessively in the small intestine, disrupting digestion and nutrient absorption. Thyroid hormones, particularly triiodothyronine (T3), play a critical role in regulating gut motility—the coordinated muscle contractions that move food along the gastrointestinal tract. Low thyroid hormone levels in hypothyroidism slow gut motility, leading to delayed clearance of intestinal contents. This stagnation allows bacteria to increase abnormally, increasing the risk of SIBO.

Hypothyroidism, especially from Hashimoto’s thyroiditis—a chronic autoimmune condition where the immune system attacks the thyroid gland, causing inflammation and gradual loss of hormone production—can thus predispose individuals to SIBO due to this impaired motility. ​

SIBO as a trigger and exacerbator of autoimmunity

SIBO also influences the immune system and the body’s inflammatory state, which can worsen autoimmune diseases like Hashimoto’s. Excess bacteria release toxins and metabolic byproducts that can damage the intestinal lining, contributing to increased gut permeability, often referred to as “leaky gut.” This condition allows bacterial fragments and inflammatory molecules to enter the bloodstream, activating the immune system and potentially triggering or worsening autoimmune responses against the thyroid.

Research indicates that people with SIBO have significantly higher odds of developing autoimmune thyroid disease compared to those without SIBO, suggesting a strong association between gut bacterial imbalance and thyroid autoimmunity.

Nutrient malabsorption and thyroid health

SIBO impairs nutrient absorption, including critical vitamins and minerals necessary for thyroid hormone synthesis and metabolism, such as vitamin B12, iron, and selenium. Deficiencies caused by SIBO-related malabsorption can further depress thyroid function or complicate treatment. Although some hypothyroid patients with SIBO maintain normal hormone replacement therapy doses, others may experience symptoms related to nutrient inadequacies that affect overall thyroid health and energy levels. ​

Clinical studies and findings

Several clinical studies highlight the prevalence and interaction of SIBO and autoimmune thyroiditis:

• Studies of Hashimoto’s patients show that over half test positive for SIBO, compared to a very low rate in healthy controls. Hypothyroidism emerged as a risk factor for SIBO due to reduced gut motility. ​
• A large retrospective cohort study found that individuals with SIBO were over twice as likely to develop Hashimoto’s thyroiditis, pointing to a potentially bidirectional relationship.
• Interestingly, levothyroxine treatment, common in hypothyroidism management, was also linked to increased SIBO incidence, although it is unclear whether the medication itself or underlying thyroid dysfunction drives this association. 

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Treating SIBO in patients with Hashimoto’s can lead to symptom improvement beyond the gut, including reduced digestive symptoms, improved nutrient status, and even reductions in thyroid antibody levels, indicating reduced autoimmune activity in some cases. 

Evidence linking the eradication of SIBO to improvement in symptoms of Hashimoto’s thyroiditis is emerging from both clinical studies and anecdotal reports. As SIBO often worsens gut inflammation, nutrient deficiencies, and immune dysregulation that contribute to autoimmune thyroid disease, clearing the bacterial overgrowth can have significant benefits for thyroid health and overall well-being.

Clinical studies and meta-analyses

A systematic review and meta-analysis of multiple studies examining antibiotic treatment for SIBO found that eradication leads to symptom improvement or resolution in approximately 68% of cases. While these studies focus primarily on gastrointestinal symptoms, they support the broader idea that treating SIBO improves systemic health in affected individuals.

Specific to Hashimoto’s, research shows a strong association between SIBO and hypothyroidism. Patients who undergo SIBO treatment—whether with antibiotics or herbal antimicrobials—often report relief not only from digestive symptoms but also improvement in thyroid-related symptoms such as fatigue and brain fog. ​

SIBO contributes to increased intestinal permeability (“leaky gut”), a state linked to chronic systemic inflammation and autoimmunity, including Hashimoto’s. Getting rid of SIBO helps restore gut barrier integrity, reducing the passage of inflammatory bacterial components into the bloodstream that can trigger or aggravate autoimmune thyroid attacks.

Patient reports and practitioner observations

Many clinicians and patients with Hashimoto’s report that after treating SIBO, symptoms such as persistent fatigue, bloating, brain fog, and joint pain improve significantly. Some even experience the ability to reduce thyroid medication dosages under medical supervision once gut health is better managed.

However, it is emphasized that SIBO can be stubborn with high relapse rates, requiring comprehensive treatment approaches including dietary changes (low FODMAP or elemental diets), antimicrobial therapy, gut lining support, and motility-improving measures to maintain remission and achieve sustained thyroid benefit. ​

While research is still evolving, evidence supports that eradicating SIBO in patients with Hashimoto’s thyroiditis improves gastrointestinal and systemic symptoms, enhances nutrient absorption, reduces immune system triggers, and may help modulate thyroid autoimmunity. For individuals with Hashimoto’s and persistent digestive issues or poor symptom control, testing and treating SIBO under medical guidance offers a promising path toward better thyroid health and quality of life.

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SIBO significantly affects and interacts with the hormonal changes during perimenopause and menopause through complex pathways involving gut health, immune function, and systemic inflammation. These stages of midlife hormonal transition in women predispose them to both altered gut motility and microbiome changes, creating an environment where SIBO is more likely to develop or worsen, which in turn contributes to the severity of menopausal symptoms. Understanding this bidirectional relationship can help women better manage their digestive and hormonal health during this life phase.

Hormonal changes during perimenopause and menopause affect gut function

Perimenopause and menopause are characterized by declining levels of estrogens and progesterone, hormones that exert wide-ranging effects beyond reproductive tissues. Estrogen receptors in the gastrointestinal tract influence motility, barrier integrity, and the immune environment of the gut. Lower estrogen during menopause slows intestinal transit time, weakening the natural “clearing” of bacteria from the small intestine. This slower motility allows bacteria to proliferate abnormally, changing the balance of your estrobolome and increasing SIBO risk.

Progesterone, which also declines during the menopausal transition, normally helps regulate smooth muscle contractions in the gut. Its reduction further delays bowel motility and contributes to functional constipation, compounding bacterial overgrowth.

Microbiome shifts in menopause contribute to SIBO

Menopause is associated with distinct changes in the gut microbiome profile, including a reduction in microbial diversity and shifts in bacterial populations. Studies report that postmenopausal women have depleted populations of beneficial bacteria such as Firmicutes, with enrichment of potentially pro-inflammatory Bacteroidetes species, altering gut ecosystem balance.

These microbial shifts can impair gut barrier function, leading to increased intestinal permeability, or “leaky gut,” which allows microbial toxins and inflammatory compounds to enter circulation. This systemic inflammation may intensify menopausal symptoms like fatigue, mood disturbances, and joint pain while worsening gut symptoms related to SIBO. ​

SIBO symptoms overlap with menopausal complaints

SIBO symptoms—including bloating, abdominal pain, diarrhea, constipation, and fatigue—mirror many complaints common in perimenopause and menopause. This overlap can delay SIBO diagnosis, as digestive symptoms may be mistaken solely for hormonal changes or attributed to irritable bowel syndrome (IBS). Yet, undiagnosed SIBO may worsen or prolong menopausal symptoms and reduce quality of life. ​

Furthermore, SIBO-related nutrient malabsorption—especially of vitamin B12, vitamin D, magnesium, and iron—can exacerbate menopausal issues such as bone density loss, cognitive decline, and decreased energy.menopausespecialists+1​

Immune system and inflammation link gut bacteria and menopause

Menopause-induced changes in estrogen modulate the immune system, often shifting women toward a more pro-inflammatory state. An overgrowth of bacteria in the small intestine due to SIBO can amplify this inflammation by activating immune cells and releasing endotoxins into the bloodstream. Higher levels of systemic inflammation are linked to worsened menopausal symptoms, including hot flashes, mood swings, and heart disease risks. ​

Clinical implications and treatment considerations

For women navigating perimenopause and menopause, recognizing the interplay between SIBO and hormonal changes is crucial. Addressing SIBO through proper testing and treatment can help alleviate digestive symptoms and improve nutrient absorption, which may in turn lessen menopausal symptom severity.

Lifestyle modifications that support gut motility and microbiome diversity—including stress reduction, regular exercise, a balanced diet rich in fiber, and avoiding medications that impair gut function—can be particularly beneficial in this demographic.

Comprehensive menopausal care should integrate gut health assessment, especially in women reporting persistent digestive symptoms or poor response to hormone therapies. In some cases, hormone replacement therapy may improve gut motility and microbiome balance, but individualized evaluation is required. ​

If you have both SIBO and a thyroid condition, it’s crucial to monitor your thyroid levels regularly. Paloma’s convenient complete at-home thyroid test kit makes this easy from home, measuring Thyroid Stimulating Hormone (TSH), Free Thyroxine (Free T4), Free Triiodothyronine (Free T3), and Thyroid Peroxidase Antibodies (TPO), with optional add-ons for Reverse T3 (RT3) and vitamin D. This comprehensive testing helps you and your healthcare provider understand your thyroid function and nutrient status, which is crucial when digestive issues like SIBO may interfere with absorption.

Managing hypothyroidism alongside SIBO is not a one-size-fits-all process. During a virtual consultation with one of Paloma’s trusted practitioners, you can develop a personalized treatment plan that addresses your unique needs, including gut health support, thyroid optimization, and strategies to restore nutrient balance. Paloma’s new Gut Health Program provides targeted guidance to manage digestive symptoms, improve nutrient absorption, and reduce inflammation. For women in perimenopause or menopause, the program also offers specialized support to address hormonal changes, gut motility challenges, and systemic inflammation, helping improve energy, digestion, and overall quality of life.

• SIBO happens when excess bacteria overgrow in the small intestine, disrupting digestion and nutrient absorption.
• Hypothyroidism slows gut motility, making people with thyroid disorders—especially Hashimoto’s—more likely to develop SIBO.
• Common SIBO symptoms include bloating, gas, abdominal pain, diarrhea or constipation, nausea, and fatigue.
• Breath testing is the most common way to diagnose SIBO, while endoscopic sampling provides the most definitive results.
• Treatment often includes antibiotics like rifaximin, herbal antimicrobials, probiotics, and targeted dietary strategies.
• Nutrient deficiencies such as vitamin B12, iron, magnesium, and vitamin D are common in SIBO and can worsen thyroid symptoms.
• Fixing the underlying cause—such as hypothyroidism, slow motility, or structural digestive issues—is essential to prevent relapse.
• During perimenopause and menopause, declining estrogen levels can slow gut motility, increasing the risk of SIBO—especially in women who also have hypothyroidism or Hashimoto’s.
• Treating SIBO in patients with Hashimoto’s may improve digestion, energy, cognitive function, and autoimmune activity.