Imbalances in the small intestinal microbiome can drive clinical consequences in the form of small intestinal bacterial overgrowth (SIBO), characterized by higher numbers of bacteria and a distribution more commonly associated with the colon.

In recent times, SIBO has been recognized as a frequent cause of common gastrointestinal conditions that share risk factors such as maldigestion and malabsorption.

Methods used for SIBO diagnosis include the aspiration and culture of small intestinal contents from the jejunum or duodenum and, more commonly, hydrogen breath tests performed using substrates such as lactulose or glucose.

SIBO definition, diagnosis and management, however, remain a matter of debate.

Saffouri and colleagues recently showed that high-throughput sequencing analysis of the small intestinal microbiome is a better predictor of gastrointestinal symptoms when compared with duodenal aspiration and culture.

First, a distinct small intestinal microbiome composition assessed using 16S ribosomal RNA-based sequencing—and not the presence or absence of SIBO assessed by aspiration and culture of small intestinal contents—allowed for differentiation between symptomatic and asymptomatic individuals (not all symptomatic individuals had dysbiosis). This meant that the results of 16S rRNA sequencing and aspirate plus culture of duodenal contents did not correlate.

In the second part of the study, Saffouri and colleagues showed that switching a group of 16 healthy individuals with a high intake of fiber to a low-fiber diet containing a high concentration of simple sugars for seven days led to bloating and abdominal pain in 80% of participants.

Neither the resolution (50% of participants) nor appearance of SIBO (50% of participants) correlated with functional gastrointestinal symptoms. More intriguingly, asymptomatic individuals on a high-fiber diet commonly met criteria for SIBO.

In contrast, changes in the small intestinal microbiome induced by a diet high in simple sugars were predictive of symptoms and related to an alteration in duodenal permeability.

In a recent news & views article, Dr. Eamonn M. M. Quigley from the Houston Methodist Hospital (United States) summarized the clinical implications of these findings as follows:

  • SIBO does not correlate with either functional gastrointestinal symptoms or small intestinal microbiome analysis using 16S rRNA sequencing.
  • The small intestinal microbiome analysis may differentiate functional gastrointestinal disorders better than the traditional duodenal culture. As most studies in this field have used quantitative cultures of jejunal aspirates and hydrogen breath tests to diagnose SIBO, the implications of studying the small intestinal microbiome via high-throughput molecular approaches to functional gastrointestinal symptoms should be further explored.
  • Simple sugars in the diet play an important role in generating functional gastrointestinal symptoms (such as bloating and abdominal discomfort) and in altering duodenal permeability.
  • Clarification is still required as to whether adaptation in the small intestinal microbiome occurs and leads to a resolution of symptoms induced by diet over time. In this regard, patients with functional gastrointestinal disorders with flatulence responded better to intermittent prebiotic administration than a restricted low-FODMAP diet, probably due to adaptation in the gut microbiome.
  • Although the role of the gut microbiota in functional IBS-type bowel disorders has usually been based on the fecal or colonic microbiome, it may be time to focus on the small intestinal microbiome.


Quigley EMM. Symptoms and the small intestinal microbiome – the unknown explored. Nat Rev Gastroenterol Hepatol. 2019. doi: 10.1038/s41575-019-0171-5.