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Review
. 2022 Jan-Dec;14(1):2154092.
doi: 10.1080/19490976.2022.2154092.

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

Consuelo Sauceda  1   2   3 , Charlie Bayne  1   2   3 , Khadijeh Sudqi  1   2   3   4   5   6 , Antonio Gonzalez  4 , Parambir S Dulai  7 , Rob Knight  3   4   5   6 , David J Gonzalez  1   2   3 , Carlos G Gonzalez  1   2   3   4   5   6
Affiliations
Review

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

Consuelo Sauceda et al. Gut Microbes. 2022 Jan-Dec.

Abstract

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.

Keywords: Inflammatory bowel disease (IBD); Multi-omics; diet; gut microbes; metabolomics; metagenomics; metaproteomics; precision medicine.

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Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
Microbe-host multi-omic targets in healthy and diseased intestinal microenvironment. Visual representation of the integration potential of multi-omics. 1) Advancements in metagenomics have identified alterations in microbial composition in IBD patients. 2) Metabolomics profile changes in the metabolic output of hosts and microbes, including short-chain fatty acids and bile acids, both of which have been linked to IBD disease severity. 3) Genomic sequencing has facilitated the identification genes that influence the development of IBD such as mutations in NOD1/2 and IL-10 inflammatory pathways. 4) Metatranscriptomics facilitates the identification of transcriptomes as a proxy for functional output differences in IBD patients. 5) Metaproteomics characterizes changes in host and microbial stool- proteins affected by IBD with the additional ability to characterize post-translational modifications.
See this image and copyright information in PMC

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