IBS and Hashimoto’s disease

25 y.o woman whose IBS and GERD cannot be controlled due to Hashimoto's disease

Thyroid hormone production

The main house cleaning mechanism of the small intestine is called MMC and is tightly regulated by the central nervous system itself, and mediated by the largest nerve of the human body, the vagus nerve. While describing this process here is of no use (it is fully detailed in MMC-SIBO chapter of the book), I need to pinpoint that there are several factors that may interfere with, delay or even inhibit completely MMC leading to bacterial overgrowth of the small intestine and as a result both upper and lower GI symptoms. Katherine fulfilled many prerequisites for MMC inhibition and thus the diagnostic panel was based on this hypothesis.

Vagus nerve innervating the large intestine

Migration motor complex

The cleaning machinery of the small intestine is regulated by the central nervous system itself. When in fasted state, muscular pulses directed by the brain forward all the debris produced by previous digestions from the small to the large intestine for elimination

Inhibited by
Leading to
Hashimoto’s disease
All day eating
Leaky gut
Several drugs

Lauritano, Ernesto Cristiano, et al. “Association between hypothyroidism and small intestinal bacterial overgrowth.” The Journal of Clinical Endocrinology & Metabolism 92.11 (2007): 4180-4184.

Pimentel, Mark, et al. “Lower frequency of MMC is found in IBS subjects with abnormal lactulose breath test, suggesting bacterial overgrowth.” Digestive diseases and sciences 47.12 (2002): 2639-2643.


Katherine was constipated since always. As far as she could remember she didn’t visit the toilet more that 3 times per week. This pattern was interrupted 5-6 times per year by a period of diarrheas, lasting no more than 3 days, and then she returned to her usual bowel habits. She is a carrier of beta-thalassemia trait and has taken lots of antibiotics, mostly due to UTI’s ans sinusitis. Besides her gut problem, two years ago she started having some upper gastrointestinal symptoms, mostly a burning sensation in the mornings and burping after meals. that’s when she started researching more about her symptoms and during an endocrinological check-up she was diagnosed with Hashimoto’s thyroiditis. When she started the thyroxine replacement therapy she thought that her constipation and gastric symptoms would resolve. But that did not happen. In fact things were getting worse month after month, and for this reason she underwent upper and lower GI endoscopies, with the only finding being a mild chronic gastritis. She tried several therapeutic schemes provided by her GP and a gastroenterologist but nothing seemed to work.

Trigger - Effect timeline
Pathogenic microbiome template

Antibiotic abuse
Further microbial deterioration

Hashimoto's thyroiditis
MMC inhibition

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Irregular contrasctions of the colon may be sometimes caused by faulty hormonal regulation

Both these symptoms stem from abnormal fermentation of dietary starch and fiber. Thelonger these molecules stay in the colonic environment, the more gas they produce

A hallmark of acid reflux, although several time the opposite (hypochlorrhydria) may be the culprit

Hashimoto’s disease may induce low stomach acid, making food preparation different and prolonging passage

All day eater
More and smaller defecation when taking macrogol
Symptoms worsening before menses
C-section and never breastfed
Hashimoto's thyroiditis
beta-thalassemia trait
GERD in the morning
Antibiotic abuse

Katherine’s results revealed a very intense SIBO produced gas signal along with a deeply disordered microflora. Besides commensal microbes whose levels were diminished, two Citrobacter species were detected in pathogenic amounts. Two many protein fragments were recovered on stool whereas several vitamin and nutrient deficiencies could be attributed to malabsorption. Finally, zonulin was recovered in very high levels indicating augmented intestinal permeability. Hashimoto’s and leaky gut are part of a vicious cycle. Thyroiditis delays MMC, leading to SIBO which in turn increases intestinal permeability and permits food antigens to get into circulation.

Actionable exam results

Citrobacter spc​

This pathogens in large amounts may explain gas and bloating​

Vitamin deficiencies​

Malabsorption probably produced by SIBO and leaky gut​

Zonulin levels​

Zonulin makes the intestinal junctions to relax and permits more improper antigens to enter the bloodstream

Probiotic sterility

Not a sign of Lactobaciili or Bifidobacteria on stool due to antibiotic abuse

Protein loss​

Gastritis and poor gastric phase leads to improper proteases function in the stomach and protein loss


Elevated numbers of small intestinal bacterial populations are to blame for GERD


In these cases the treatment lasts for at least 3 months, during which rifaximine is provided intermittently. It is also crucial that the patient is given a very specific and strict dietary program consisting of gut nourishing meals along with clear fasting periods which will help restore the small intestinal environment and physicochemical properties of the epithelium.

Follow up

The reason Katherine kept coming back for the next 9 months was to ensure she was on the right treatment. She did not want to experience the same symptoms again. Mild flare ups were not concerning.

Theodoros Prevedoros
With extensive experience evaluating over 3000 cases in various specialties, including gastroenterology, pediatrics, and endocrinology, Theodoros has collaborated with more than 25 doctors from Greece and Cyprus and over 10 laboratories worldwide.

With a background in Chemistry and Biochemistry from the National and Kapodistrian University of Athens, Theodoros brings a wealth of knowledge in functional medicine and advanced treatments to his role. He possesses exceptional skills in analysis, pattern recognition, diagnostic translation, and storytelling. He is also FMU certified in Functional Medicine and has received training in advanced treatments from the Saisei Mirai Clinic in Japan.