Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study.

Gut
Adam G ClooneyMarcus J Claesson

Abstract

The microbiome contributes to the pathogenesis of inflammatory bowel disease (IBD) but the relative contribution of different lifestyle and environmental factors to the compositional variability of the gut microbiota is unclear. Here, we rank the size effect of disease activity, medications, diet and geographic location of the faecal microbiota composition (16S rRNA gene sequencing) in patients with Crohn's disease (CD; n=303), ulcerative colitis (UC; n = 228) and controls (n=161), followed longitudinally (at three time points with 16 weeks intervals). Reduced microbiota diversity but increased variability was confirmed in CD and UC compared with controls. Significant compositional differences between diseases, particularly CD, and controls were evident. Longitudinal analyses revealed reduced temporal microbiota stability in IBD, particularly in patients with changes in disease activity. Machine learning separated disease from controls, and active from inactive disease, when consecutive time points were modelled. Geographic location accounted for most of the microbiota variance, second to the presence or absence of CD, followed by history of surgical resection, alcohol consumption and UC diagnosis, medications and diet with mos...Continue Reading

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Citations

Dec 1, 2020·Gastroenterology·Fergus ShanahanPaul W O'Toole
Jan 17, 2021·Nutrients·Charlotte M VerburgtJohan E Van Limbergen
Feb 5, 2021·Frontiers in Molecular Biosciences·Stanislav N IablokovAlexander V Tyakht
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Mar 6, 2021·Microbial Ecology·Rachel S FitzgeraldMarcus J Claesson
Apr 4, 2021·International Journal of Molecular Sciences·Laila Aldars-GarcíaJavier P Gisbert
Jun 25, 2021·Frontiers in Immunology·Anna TorunBeata Pyrzynska
Jun 26, 2021·New Microbes and New Infections·P ThomsonC Bay
Aug 6, 2021·Frontiers in Microbiology·Sayf Al-Deen HassounehShibu Yooseph
Mar 19, 2021·Journal of Crohn's & Colitis·Claudio FiocchiUNKNOWN Scientific Workshop Steering Committee
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Nov 10, 2021·Alimentary Pharmacology & Therapeutics·Shiva T RadhakrishnanHorace R T Williams
Aug 9, 2021·The Journal of Investigative Dermatology·Siobhán McCarthyPaul W O'Toole

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Datasets Mentioned

BETA
PRJNA414072

Methods Mentioned

BETA
amplicon sequencing
PCR
DNA assay
ELISA
PCA

Software Mentioned

vegan
made4
QIIME script
MetagenomeSeq
dynamicTreeCut
USEARCH
SPINGO
ChimeraSlayer
fastq
R package ‘ phyloseq ’

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