Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease

Alba Boix-Amorós, Hilary Monaco, Elisa Sambataro, Jose C. Clemente

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.

Original languageEnglish
Article number2107866
JournalGut Microbes
Issue number1
StatePublished - 2022


  • IBD
  • flow cytometry
  • metabolomics
  • microbial therapeutics
  • microbiome
  • networks
  • technology
  • time series


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