Related Experiment Video
Updated: Sep 9, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Relationship Between Hypothyroidism, Risk of Small Intestinal Bacterial Overgrowth, and Duodenal Microbiome
Margaret Wei1, Sepideh Mehravar2, Gabriela Leite2
1Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai, Los Angeles, CA 90048, USA.
Context:
There is an association between hypothyroidism and small intestinal bacterial overgrowth (SIBO), but the exact mechanistic link between these 2 conditions is not fully elucidated.
Objective:
We evaluate the incidence and risks of subsequently developing SIBO, and changes in small bowel microbial populations, in subjects with hypothyroidism or autoimmune thyroiditis.
Design And Outcome Measures:
Duodenal aspirates from REIMAGINE study subjects with a history of hypothyroidism (hypothyroid group, N = 49) and controls (N = 323) underwent 16S rRNA sequencing (MiSeq, Illumina); a subset also underwent metagenomic sequencing (NovaSeq6000, Illumina). Separately, the TriNetX Analytics platform was used to evaluate 10-year cumulative incidences and relative risk (RR) of developing SIBO in subjects with hypothyroidism (unspecified etiology [HUE]), and a subset with autoimmune thyroiditis, vs propensity score matched control groups.
Results:
Among REIMAGINE subjects, SIBO prevalence was higher in the hypothyroid group (32.65%) vs controls (15.17%). In the TriNetX analysis, 10-year cumulative incidences of SIBO were higher in HUE (RR = 2.20) and autoimmune thyroiditis (RR = 2.40) subjects vs matched controls. However, these risks appeared to be mitigated both in HUE (RR = 0.33) and autoimmune thyroiditis (RR = 0.78) subjects taking levothyroxine. Analyzing the duodenal microbiome, genus Neisseria was part of the core microbiome in the hypothyroid group (Hypo+/SIBO-, Hypo+/SIBO+) but not in nonhypothyroid subjects (Hypo-/SIBO-, Hypo-/SIBO+). Increased prevalence of Gram-negative coliforms occurred in both SIBO+ groups, but Escherichia/Shigella formed part of the core in nonhypothyroid subjects (Hypo-/SIBO+), whereas Klebsiella species were prevalent in hypothyroid group subjects with SIBO (Hypo+/SIBO+).
Conclusion:
These findings suggest there is an increased risk for development of SIBO in individuals with a history of hypothyroidism that may be ameliorated by treatment, and may involve specific Gram-negative coliforms.
More Related Videos
Related Concept Videos
Irritable Bowel Syndrome I: Introduction
IBS is a chronic condition that can persist over a long period or recur frequently.
The pathogenesis of IBS involves a complex interplay of the following factors:
Altered...
Anatomy of the Intestines
Small Intestines
The small intestine is an ~7 meter-long tube with an inner diameter of just 2.5 cm. Since most nutrients are absorbed here, the inner lining of the...
Bacterial Flora of the Large Intestine
The normal gut flora of the colon plays a critical role in generating essential vitamins such as vitamins K, B5, and B7.
Inflammatory Bowel Disease III: Diagnostic Studies and Management I-Nutritional Therapy
Diagnostic studies
A colonoscopy is the definitive screening test, distinguishing ulcerative colitis from other colon diseases with similar symptoms. During a colonoscopy test, inflamed mucosa with exudate ulcerations can be observed, and biopsies are taken to determine the histologic characteristics of the...
Histology of the Small Intestine
The intestinal lining features transverse folds called circular folds, each housing fingerlike projections known as intestinal villi. These villi are covered by a layer of simple columnar epithelium, also referred to as...
Chronic Bowel Disorders: Introduction
Irritable Bowel Syndrome (IBS) is a common disorder affecting the gastrointestinal tract. The distinctive feature is recurrent abdominal pain associated with altered bowel movements, manifesting as constipation, diarrhea, or fluctuating between both. The...

