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Project “Minute for IBD” in Croatia – translational approach to microbiota composition assessment

Inflammatory bowel disease (IBD) is a chronic gastrointestinal disorder with increased incidence. The onset of the disease is mainly associated with the immune status, gut microbiota and food intake. The current scientific knowledge of specific triggers and diagnostic markers is limited ; therefore, new data on gut microbiota, inflammatory, endocrine and nutritional status are required to better understand the IBD pathophysiology and ultimately support stratification of patients and initiation of appropriate therapy. In the translational project (Assessment of Microbiota, Inflammatory Markers, Nutritional and Endocrinological Status in IBD Patients ; Acronym Minute for IBD) we are exploring host-gut microbiota interactions in order to define novel strategies for the management of IBD. Stool, intestine biopsies and blood samples from 40 newly diagnosed IBD patients and 20 non-IBD control individuals are collected and their nutritional status recorded. This work has been fully supported by the Croatian Science Foundation under the project number [5467]. To characterize the composition of the microbiota in collected samples next-generation sequencing (MiSeq, Illumina) is used. As DNA isolation from complex biological samples is a major step in obtaining high quality DNA, as the first step, the utility of commercially available systems (OMNIgene.GUT stool collection system, and DNA extraction kits: MP Biomedicals, QIAGEN, MO BIO) was assessed in healthy volunteers. It has been demonstrated that DNA yield and quality varied between DNA extraction kits (MP Biomedicals>QIAGEN>MO BIO). Although donor-specific bacterial diversity was maintained irrespective of the collection, storage or extraction method used, kit-based trends were observed displaying different levels of abundance among the most prevalent families, notably Bacteroidaceae and Lachnospiraceae. These preliminary results showed that commercially available systems OMNIgene.GUT and MP Biomedicals are convenient and reliable tools for the assessment of human faecal microbiota composition. This clinical research study deals with the cutting-edge, hot topics (microbiota composition) and uses state-of-the art sensitive methodologies (biomarkers determination). It will provide valuable insights that will be applied for better IBD patients’ stratification into specific therapeutic and nutritional interventions.

inflammatory bowel disease; gut microbiota; human faecal samples; DNA extraction; 16S rRNA gene sequencing

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