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Marcus Claesson

Associate Professor, University College Cork and CEO at SeqBiome, Ireland

After degrees in chemical engineering and bioinformatics at Chalmers University of Technology, Marcus completed his PhD and postdocs at University College Cork analysing Lactobacillus genomes and age-related microbiomes. He is now an Associate Professor in Bioinformatics at APC Microbiome Ireland, researching the microbiota in inflammatory bowel disease. He currently coordinates the MSc in Bioinformatics and recently chaired the EU COST Action ML4Microbiome aiming to optimize and standardize machine learning in microbiome science. He has over 90 publications and was among the top 0.3% most cited scientists in 2021. In 2020, Marcus co-founded SeqBiome, providing high-quality microbiome analysis for industry and academia.

Disentangling the microbiome of IBD and the role of machine learning

Crohn’s disease and ulcerative colitis are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. Our team has reported disturbances in the microbiome in a cross-sectional study of biopsies from inflamed and non-inflamed colonic mucosa, and longitudinally using stool samples as intestinal proxy. Using cutting-edge combinatory machine learning approaches, we found that faecal microbiome disturbances were associated with active disease rather than remission, and that multi-omics can predict future flares within 4 years from endoscopy. The use of machine learning is, however, fraught with sub-optimal use and several analytical challenges. These have recently been outlined and partly addressed by the EU COST Action ML4Microbiome, whose main outcomes also will be summarised.