Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders

George B. Saffouri, Robin R. Shields-Cutler, Jun Chen, Yi Yang, Heather R. Lekatz, Vanessa L. Hale, Janice M. Cho, Eric J. Battaglioli, Yogesh Bhattarai, Kevin J. Thompson, Krishna K. Kalari, Gaurav Behera, Jonathan C. Berry, Stephanie A. Peters, Robin Patel, Audrey N. Schuetz, Jeremiah J. Faith, Michael Camilleri, Justin L. Sonnenburg, Gianrico FarrugiaJonathan R. Swann, Madhusudan Grover, Dan Knights, Purna C. Kashyap

Research output: Contribution to journalArticlepeer-review

40 Scopus citations


Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics. Here we show that SIBO based on duodenal aspirate culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small intestinal microbial diversity while increasing small intestinal permeability. Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment.

Original languageEnglish (US)
Article number2012
JournalNature communications
Issue number1
StatePublished - Dec 1 2019

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)


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