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Mucosa-associated Microbiota in the Gastrointestinal Tract of Adult, Newly Diagnosed, Treatment-naïve Inflammatory Bowel Disease (IBD) Patients

Background: Inflammatory bowel disease (IBD) and its two most common disease subtypes ; Crohn's disease (CD) and ulcerative colitis (UC) are suggested to be related to gut dysbiosis caused by the persistent imbalance of the microbiota. Advances in the next-generation sequencing enable culture-independent analysis of the complex microbial communities and provide insight into gastrointestinal tract and its ecological landscape. The aim of this study was to determine differences in mucosa-associated microbiota composition in adult, newly diagnosed and treatment-naïve IBD patients and control patients with irritable bowel syndrome (IBS). Methods: Mucosal tissue samples were collected from both groups of patients at 6 distinct positions along the gut, as part of diagnostic colonoscopy examination prior to the initiation of treatment, followed by snap-freezing. DNA was extracted using MasterPure DNA purification kit (Epicentre). The composition of gut microbiota from mucosa was determined by amplification and sequencing of bacterial 16S rRNA gene using Illumina MiSeq according to manufacturer- recommended protocols. Raw sequencing files were processed using QIIME 1 pipeline and Operational Taxonomic Units (OTUs) were assigned using the vsearch algorithm and PyNast alignment against the GreenGenes database (version 13_8, May 2013). Subsequent processing and analysis was done using ALDEx2 R (Gloor and Reid. Can. J. Microbiol. 703 ; 2016). Results: The microbiota composition of mucosa sampled at 6 positions (from terminal ileum to rectum) was analyzed at the family level. Contrary to our expectations, no significant position- dependent differences in taxa abundance in individual patients were determined. The major enterotypes (Bacteroidetes- and Prevotella- dominating) were observed among individuals. Samples from inflamed areas of the gut displayed altered abundance of a limited number of families (decrease of Verrucomicrobiaceae and Rikenellaceae, increase of Pasterurellaceae), albeit with modest effect sizes. Alpha-diversity for individuals diagnosed with UC was decreased. Differences in microbiota abundance were most pronounced between two IBD phenotypes – UC and CD with UC having increased abundance of Neisseriaceae, Pasterurellaceae, Peptococcaceae, Peptostreptococcaceae, Turicibacteriaceae, Veillonelaceae, S24-7 and shifts in several of the low abundance families. Decrease in Verrucomicrobiaceae was found in CD. Conclusion: Preliminary results indicate distinct individual gut mucosa bacterial profiles, independent of the sampling position. Microbiota differences between disease phenotypes were found to be more profound than between inflammation status of the colon mucosa.

microbiota ; IBD ; IBS

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