Microbiome Sampling in GI Disease With a Focus on Small Intestinal Microbial Assessment

Current guidelines (AGA Clinical Practice Update, 2020) report the definition of SIBO as a clinical entity lacks precision and consistency; it is a term generally applied to a clinical disorder where symptoms, clinical signs, and/or laboratory abnormalities are attributed to changes in the numbers of bacteria or in the composition of the bacterial population in the small intestine. To date, there is unlimited knowledge regarding the diagnostic criterion which has been limited by nonspecific and nonsensitive testing such as breath tests. Breath tests have a limited use in patients with IBS-D who inherently have increased gut transit time rendering the testing invalid for accurately measuring small intestinal bacteria. Additionally, the relationship between SIBO and symptoms in patients without obvious risk factors (such as anatomical changes due to surgery) is unknown. The investigators study aims to investigate the microbial landscape of the small intestine in healthy patients and those with GI disease (suspected or diagnosed) undergoing an upper endoscopy by collecting an aspirate of patient small intestinal fluid and studying it.

Inclusion criteria

• Age >18years
• Patients seen at Stanford University Digestive Health Center who are scheduled for an upper endoscopy as part of their Standard Of Care

Exclusion criteria

Children (under age 18years) Pregnant Women and Fetuses Neonates (0 - 28 days) Impaired Decision Making Capacity