The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease

Jonathan P Segal, Benjamin H Mullish, Mohammed Nabil Quraishi, Animesh Acharjee, Horace R T Williams, Tariq Iqbal, Ailsa L Hart, Julian R Marchesi

Research output: Contribution to journalReview articlepeer-review

21 Citations (Scopus)
186 Downloads (Pure)


The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient’s genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn’s disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD.

With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingly also the alterations in microbiota function that accompany these. Technologies such as metagenomics, metataxomics, metatranscriptomics, metaproteomics and metabonomics are therefore allowing us a deeper understanding of the role of the microbiota in IBD. Furthermore, the integration of these systems biology technologies through advancing computational and statistical techniques are beginning to understand the microbiome interactions that both contribute to health and diseased states in IBD.

This review aims to explore how such systems biology technologies are advancing our understanding of the gut microbiota, and their potential role in delineating the aetiology, development and clinical care of IBD.
Original languageEnglish
Pages (from-to)1-13
Number of pages13
JournalTherapeutic Advances in Gastroenterology
Early online date24 Jan 2019
Publication statusPublished - 2019

Bibliographical note

Funding Information:
The Division of Integrative Systems Medicine and Digestive Disease at Imperial College, London, UK receives financial support from the National Institute of Health Research Imperial Biomedical Research Centre based at Imperial College Healthcare NHS Trust and Imperial College London. BHM is the recipient of a UK Medical Research Council Clinical Research Training Fellowship (grant reference: MR/ R000875/1).

Publisher Copyright:
© The Author(s), 2019.


  • bioinformatics
  • genomics
  • gut microbiota
  • inflammatory bowel diseases
  • interactome
  • metagenomics
  • metatranscriptomics metabonomics
  • proteomics


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