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Gut microbiome composition and risk factors in a large cross-sectional IBS cohort
  1. Melissa Agnello1,
  2. Lauren N Carroll1,
  3. Nabeel Imam2,
  4. Rodolfo Pino2,
  5. Christina Palmer1,
  6. Ignacio Varas3,
  7. Claire Greene1,
  8. Maureen Hitschfeld4,
  9. Sarah Gupta1,
  10. Daniel E Almonacid1,
  11. Michael C Hoaglin1
  1. 1Medical Affairs, uBiome, San Francisco, California, USA
  2. 2Medical Affairs, uBiome, Santiago, Chile
  3. 3Bioinformatics, uBiome, Santiago, Chile
  4. 4Data Science, uBiome, Santiago, Chile
  1. Correspondence to Dr Michael C Hoaglin; mike{at}


Objective Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is difficult to diagnose and treat due to its inherent heterogeneity and unclear aetiology. Although there is evidence suggesting the importance of the microbiome in IBS, this association remains poorly defined. In the current study, we aimed to characterise a large cross-sectional cohort of patients with self-reported IBS in terms of microbiome composition, demographics, and risk factors.

Design Individuals who had previously submitted a stool sample for 16S microbiome sequencing were sent a comprehensive survey regarding IBS diagnosis, demographics, health history, comorbidities, family history, and symptoms. Log ratio-transformed abundances of microbial taxa were compared between individuals reporting a diagnosis of IBS without any comorbidities and individuals reporting no health conditions. Univariable testing was followed by a multivariable logistic regression model controlling for relevant confounders.

Results Out of 6386 respondents, 1692 reported a diagnosis of IBS without comorbidities and 1124 reported no health conditions. We identified 3 phyla, 15 genera, and 19 species as significantly associated with IBS after adjustment for confounding factors. Demographic risk factors include a family history of gut disorders and reported use of antibiotics in the last year.

Conclusion The results of this study confirm important IBS risk factors in a large cohort and support a connection for microbiome compositional changes in IBS pathogenesis. The results also suggest clinical relevance in monitoring and investigating the microbiome in patients with IBS. Further, the exploratory models described here provide a foundation for future studies.

  • irritable bowel syndrome
  • intestinal microbiology
  • genetic testing
  • molecular biology
  • stool markers

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  • MA and LNC contributed equally.

  • Contributors SG, DEA, MH, and CP were involved in conceptualising the study. LNC, SG, DEA, and MCH supervised the work. Survey design and data collection were completed by MCH and MH, with support from CG. Bioinformatics and statistical analyses were led by NI, with key contributions from RP, IV, and MH. MA, LNC, and NI guided the data interpretation along with CG, MH, RP, DEA, and MCH. LNC and MA led the efforts to write and edit the manuscript. NI, CP, MH, and MCH wrote portions of the original draft, and all authors reviewed the final draft for edits prior to submission.

  • Funding uBiome funded the study design, collection, analysis and interpretation of the data; writing of the paper; and decision to submit for publication. Manuscript publication was funded by Psomagen.

  • Competing interests All of the authors were employees or contractors of uBiome at the time of this work and received compensation. Some authors have issued and/or pending patents in relation to this work: patent US 9,703,929 issued, patent US 10,242,160 issued, patent US 10,287,639 issued, patent US 10,294,532 issued, patent US 10,331,857 issued, patent US 10,360,346 issued, patent US 2017/0270268 pending, patent US 2018/0137239 pending, and patent US 2019/0050534 pending. All authors have a patent pending in relation to this work: US provisional application No 62/968,251, Gut microbiome composition and risk factors in a large cross-sectional IBS cohort.

  • Patient consent for publication Not required.

  • Ethics approval The study was approved by Asentral IRB (#2016-440).

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data availability statement Data are available upon reasonable request. Please contact the corresponding author.