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

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 multi...

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Autores principales: Sauceda, Consuelo, Bayne, Charlie, Sudqi, Khadijeh, Gonzalez, Antonio, Dulai, Parambir S., Knight, Rob, Gonzalez, David J., Gonzalez, Carlos G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9746627/
https://www.ncbi.nlm.nih.gov/pubmed/36503356
http://dx.doi.org/10.1080/19490976.2022.2154092
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author Sauceda, Consuelo
Bayne, Charlie
Sudqi, Khadijeh
Gonzalez, Antonio
Dulai, Parambir S.
Knight, Rob
Gonzalez, David J.
Gonzalez, Carlos G.
author_facet Sauceda, Consuelo
Bayne, Charlie
Sudqi, Khadijeh
Gonzalez, Antonio
Dulai, Parambir S.
Knight, Rob
Gonzalez, David J.
Gonzalez, Carlos G.
author_sort Sauceda, Consuelo
collection PubMed
description 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.
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spelling pubmed-97466272022-12-14 Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease Sauceda, Consuelo Bayne, Charlie Sudqi, Khadijeh Gonzalez, Antonio Dulai, Parambir S. Knight, Rob Gonzalez, David J. Gonzalez, Carlos G. Gut Microbes 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. Taylor & Francis 2022-12-11 /pmc/articles/PMC9746627/ /pubmed/36503356 http://dx.doi.org/10.1080/19490976.2022.2154092 Text en © 2022 The Author(s). Published with license by Taylor & Francis Group, LLC. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
Sauceda, Consuelo
Bayne, Charlie
Sudqi, Khadijeh
Gonzalez, Antonio
Dulai, Parambir S.
Knight, Rob
Gonzalez, David J.
Gonzalez, Carlos G.
Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease
title Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease
title_full Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease
title_fullStr Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease
title_full_unstemmed Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease
title_short Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease
title_sort stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9746627/
https://www.ncbi.nlm.nih.gov/pubmed/36503356
http://dx.doi.org/10.1080/19490976.2022.2154092
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