Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease

Shixian Hu, Arno R. Bourgonje, Ranko Gacesa, Bernadien H. Jansen, Johannes R. Björk, Amber Bangma, Iwan J. Hidding, Hendrik M. van Dullemen, Marijn C. Visschedijk, Klaas Nico Faber, Gerard Dijkstra, Hermie J. M. Harmsen, Eleonora A. M. Festen, Arnau Vich Vila, Lieke M. Spekhorst and Rinse K. Weersma ()
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Shixian Hu: University of Groningen, University Medical Center Groningen
Arno R. Bourgonje: University of Groningen, University Medical Center Groningen
Ranko Gacesa: University of Groningen, University Medical Center Groningen
Bernadien H. Jansen: University of Groningen, University Medical Center Groningen
Johannes R. Björk: University of Groningen, University Medical Center Groningen
Amber Bangma: University of Groningen, University Medical Center Groningen
Iwan J. Hidding: University of Groningen, University Medical Center Groningen
Hendrik M. van Dullemen: University of Groningen, University Medical Center Groningen
Marijn C. Visschedijk: University of Groningen, University Medical Center Groningen
Klaas Nico Faber: University of Groningen, University Medical Center Groningen
Gerard Dijkstra: University of Groningen, University Medical Center Groningen
Hermie J. M. Harmsen: University of Groningen, University Medical Center Groningen
Eleonora A. M. Festen: University of Groningen, University Medical Center Groningen
Arnau Vich Vila: University of Groningen, University Medical Center Groningen
Lieke M. Spekhorst: University of Groningen, University Medical Center Groningen
Rinse K. Weersma: University of Groningen, University Medical Center Groningen

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract Disrupted host-microbe interactions at the mucosal level are key to the pathophysiology of IBD. This study aimed to comprehensively examine crosstalk between mucosal gene expression and microbiota in patients with IBD. To study tissue-specific interactions, we perform transcriptomic (RNA-seq) and microbial (16S-rRNA-seq) profiling of 697 intestinal biopsies (645 derived from 335 patients with IBD and 52 from 16 non-IBD controls). Mucosal gene expression patterns in IBD are mainly determined by tissue location and inflammation, whereas the mucosal microbiota composition shows a high degree of individual specificity. Analysis of transcript-bacteria interactions identifies six distinct groups of inflammation-related pathways that are associated with intestinal microbiota (adjusted P

Date: 2024
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DOI: 10.1038/s41467-024-45855-2

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