We know that the gut microbiome is thought to be involved in the pathogenesis of functional gastrointestinal disorders. However, even though underlying mechanisms are poorly understood, small intestinal bacterial overgrowth (SIBO) could contribute to explaining some gastrointestinal symptoms in patients with these conditions. The field’s primary challenges include characterizing the small intestinal microbiome and exploring to what extent diet-driven changes might help mitigate symptoms in patients with functional gastrointestinal disorders.

A new study, led by Dr. Purna C. Kashyap from the Mayo Clinic in Rochester (Minnesota, USA), reveals that the small intestinal microbiome is altered in patients with gastrointestinal symptoms, which can be triggered through diet in a microbiota-dependent manner.

The researchers characterized the small intestinal microbiota of 164 patients, which was obtained through quantitative duodenal aspirate culture. Patients with diarrhea, abdominal pain and bloating (n = 126) showed a significant alteration in the duodenal aspirate microbiome when compared with healthy controls (n = 34). Specifically, the small intestinal microbiome from symptomatic patients was characterized by lower alpha diversity (observed species within the sample), richness (number of species), and evenness (distribution of species), alongside a decrease in Porphyromonas, Prevotella and Fusobacterium.

The composition of the small intestine microbiome in symptomatic patients showed a high level of heterogeneity when compared with healthy controls. Furthermore, while 29% of symptomatic patients had a dysbiosis-like duodenal microbiome based on a dysbiosis index, 71% were found to harbor a healthy-like duodenal microbiome when evaluated for its relationship with healthy controls’ microbiome diversity.

The authors also explored which factors could explain the observed changes in the duodenal microbiome in symptomatic patients. Patients’ advanced age, antibiotic and proton pump inhibitor use and history of gastrointestinal surgery contributed to changes in the duodenal microbiome. However, patients’ sex, body mass index, and the presence of SIBO were not associated with the altered small intestine microbiome. As regards SIBO, 66 of the 126 symptomatic patients tested positive for this.

The effects of changes in the small intestine microbial composition on duodenal microbiome functional diversity were also predicted through 16S ribosomal ribonucleic acid, using a bioinformatics software package. Pathways related to oxidative stress, biosynthesis of siderophores—involved in allowing bacteria to transport iron across the cell membrane—and mono- and disaccharide metabolism were enriched in symptomatic patients.

Saffouri and colleagues went a step further and explored whether diet could trigger gastrointestinal symptoms in a microbiota-dependent manner. At baseline, a subset of individuals eating a high-fiber diet had SIBO but did not show gastrointestinal symptoms and alterations in their duodenal microbiome composition.

In contrast, when the participants’ diet was switched from a high-fiber diet to a high simple-sugar diet for 7 days, increased small intestinal permeability was shown, along with the appearance of gastrointestinal symptoms and decreased acetate and butyrate associated with decreased microbial diversity. Thus, the presence of SIBO is not related to gastrointestinal symptoms and diet is a major factor that contributes to the observed increased small bowel bacterial counts.

These findings support the known negative effects of a low-fiber diet on microbial diversity and highlights the importance of considering diet modification as a therapeutic strategy in patients with functional gastrointestinal disorders.

In conclusion, this study has characterized the small intestine microbiome in the context of functional gastrointestinal disorders. Although an altered duodenal microbiome correlates with functional gastrointestinal symptoms, the presence of SIBO is not necessarily associated with symptoms and can be the outcome of dietary preference.



Saffouri GB, Shields-Cutler RR, Chen J, et al. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nat Commun. 2019; 10(1):2012. doi: 10.1038/s41467-019-09964-7.