An underactive thyroid or hypothyroidism is associated with a higher risk of developing small intestinal bacterial overgrowth (SIBO), according to new data presented at this year’s annual meeting of the Endocrine Society. This association was particularly pronounced among individuals with Hashimoto’s disease, also known as autoimmune thyroiditis
However, the results also showed that this risk appears to be mitigated in those taking thyroid medications.
“We know that the gut and the thyroid are integrally linked, and the microbiome plays a critical role in this crosstalk,” said Gabriela Leite, PhD, a research associate at Cedars-Sinai Medical Center and a co-author of the study. “While previous studies have shown that there are associations between hypothyroidism and SIBO – one of the primary diseases that leads to changes in the small bowel microbiome, the precise cross-relation between the two conditions is unknown.”
Dr. Leite noted that some studies have suggested that hypothyroidism may result in decreased gut motility, which in turn heightens the risk for SIBO. “Now, looking into the other direction, where changes in the microbiome contribute to thyroid dysfunction, although a plausible hypothesis--considering different studies showing a strong association between changes in the microbiome and endocrine diseases--our data cannot, at this point, support this route,” she said. “More data needs to be analyzed to support this path, and we plan to investigate that.”
The relationship between SIBO and hypothyroidism was investigated in a cohort of 49 individuals with hypothyroidism and 323 controls, who had undergone upper endoscopy without colon prep. Small bowel fluid samples were analyzed from all participants and DNA sequencing was performed to identify microbial species.
There was a significantly increased prevalence of SIBO among individuals with hypothyroidism, and this difference was independent of sex (OR=2.71, CI=1.39-5.30, P=0.005). As SIBO is a major driver of duodenal microbiome changes, the cohort was divided into four groups for microbial analysis: SIBO-positive with hypothyroidism, SIBO-negative with hypothyroidism, SIBO-positive without thyroid disease, and SIBO-negative without thyroid disease.
The analysis showed that patterns of bacteria varied, depending on a person's thyroid status and co-occurrence of SIBO. The researchers found that genus Neisseria was part of the core microbiome in persons with hypothyroidism but not in those without hypothyroidism. The Gram-negative profile of the core microbiome also appeared to be differ between the two group. Persons who were SIBO-positive with hypothyroidism had a core microbiome containing Klebsiella, which is associated with SIBO, while Escherichia, a genus also associated with SIBO, was part of the core duodenal microbiome in persons who were SIBO-positive without thyroid disease.
It remains unclear why this risk is even more pronounced for those with autoimmune thyroiditis. Dr Leite explained that they don’t yet have a mechanistic explanation for it. “However, we do know that the mechanism implicated in the pathogenesis of SIBO following acute gastroenteritis is through molecular mimicry,” she said, “Which is a mechanism where similarities between foreign molecules trigger cross-reactive immune responses, leading to autoimmune diseases.
As an example, it has been shown that antibodies to the cytolethal distending toxin subunit B, a bacterial toxin, cross-react with vinculin, a cytosolic protein found in the enteric nervous system. Anti-CdtB antibody levels have been shown to correlate with the development of SIBO.
“This raises the question of whether molecular mimicry may also explain, at least in part, the association between SIBO and autoimmune hypothyroidism,” she said, adding that previous studies by other groups observed multiple microorganisms with homology to TPO and thyroglobulin.
But at this point, a cause-and-effect relationship between hypothyroidism and SIBO cannot be proven. “However, it is well understood that patients with thyroid disease can experience unexplained gastrointestinal symptoms” she said. “Based on these findings, it is possible to suggest that SIBO may explain some of these symptoms, and doctors could consider a breath test to evaluate for this condition.”
“Small Intestinal Bacterial Overgrowth Associated With Higher Risk of Hashimoto’s Thyroiditis, presented July 12, 2025. ENDO 2025, the annual meeting of The Endocrine Society
Illustration by April Brust
