Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease

Consuelo Sauceda, Charlie Bayne, Khadijeh Sudqi, Antonio Gonzalez, Parambir S. Dulai, Rob Knight, David J. Gonzalez, Carlos G. Gonzalez

Research output: Contribution to journalReview articlepeer-review


Inflammatory Bowel Disease (IBD) is a chronic immune-mediated inflammatory disease of the gastrointestinal tract that is a growing public burden. Gut microbes and their interactions with hosts play a crucial role in disease pathogenesis and progression. These interactions are complex, spanning multiple physiological systems and data types, making comprehensive disease assessment difficult, and often overwhelming single-omic capabilities. Stool-based multi-omics is a promising approach for characterizing host-gut microbiome interactions using deep integration of technologies such as 16S rRNA sequencing, shotgun metagenomics, meta-transcriptomics, metabolomics, and metaproteomics. The wealth of information generated through multi-omic studies is poised to usher in advancements in IBD research and precision medicine. This review highlights historical and recent findings from stool-based muti-omic studies that have contributed to unraveling IBD’s complexity. Finally, we discuss common pitfalls, issues, and limitations, and how future pipelines should address them to standardize multi-omics in IBD research and beyond.

Original languageEnglish (US)
Article number2154092
JournalGut Microbes
Issue number1
StatePublished - 2022


  • Inflammatory bowel disease (IBD)
  • Multi-omics
  • diet
  • gut microbes
  • metabolomics
  • metagenomics
  • metaproteomics
  • precision medicine

ASJC Scopus subject areas

  • Gastroenterology
  • Microbiology (medical)
  • Infectious Diseases
  • Microbiology


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