Underactive thyroid linked to increased risk of small intestinal bacterial overgrowth

People with an underactive thyroid may have an increased risk of developing small intestinal bacterial overgrowth (SIBO), a risk that may be reduced with thyroid hormone treatment, according to a study being presented Saturday at ENDO 2025, the Endocrine Society’s annual meeting in San Francisco, Calif.

We now know that people with hypothyroidism, especially those with autoimmune thyroiditis, are more likely to develop SIBO, but this risk appear to be mitigated in those taking thyroid medications.” 

Ruchi Mathur, M.D., Director of the Diabetes Outpatient Treatment and Education Center and Director of Clinical Operations of Medically Associated Science and Technology, at Cedars-Sinai in Los Angeles, Calif.

Mathur said their research also suggests there may be a microbiological mechanism driving this association, which could lead to more personalized treatments. 

The researchers investigated the relationship between SIBO and hypothyroidism in people older than 18 who previously underwent upper endoscopy without colon prep and reported living with hypothyroidism as well as controls. Subjects were recruited through their flagship REIMAGINE study.

They analyzed small bowel fluid samples from 49 people with hypothyroidism and 323 without the condition and performed DNA sequencing to identify microbial species. The results showed that people with hypothyroidism had a significantly higher prevalence of SIBO compared to controls (33% vs. 15%).

Mathur and colleagues then further evaluated four groups: SIBO-positive with hypothyroidism, SIBO-negative with hypothyroidism, SIBO-positive without thyroid disease, and SIBO-negative without thyroid disease.

The analysis showed different patterns of bacteria in the gut depending on a person’s thyroid status and co-occurrence of SIBO.

Separately, they performed a large-scale analysis of medical records from the TriNetX database, which looked at the 10-year risks of developing SIBO in people with hypothyroidism or autoimmune thyroiditis compared to matched controls. The risks were also mitigated in people taking levothyroxine.

“Results showed the risk of developing SIBO in subjects with hypothyroidism is 2.2 times more than the risk in a matched control cohort and was 2.4 times higher in those with autoimmune thyroiditis compared to a matched control group. This echoes our findings in the REIMAGINE cohort,” noted the study’s presenting author, Margaret Wei, M.D., of the Cedars-Sinai Medical Center Endocrine Fellowship Program.

“These findings open the door to new screening and prevention strategies. For example, doctors may begin to monitor thyroid health more closely in patients with SIBO, and vice versa. It also supports the idea that improving gut health could have far-reaching effects beyond digestion, possibly even helping to prevent autoimmune diseases, such as Hashimoto’s,” Mathur said. “As research continues, this could lead to more personalized care and earlier interventions for at-risk individuals.”