Jeroen Raes
Professor
KU Leuven - VIB
Prof. Jeroen Raes is full professor at KU Leuven since 2013. He has a substantial track record in microbiome research and has been pioneering the analysis and integration of meta-omics datasets (metagenomics, metatranscriptomics, metaproteomics, meta-metabolomics) with environmental, clinical and dietary data. He was/is involved in the FP7 MetaHIT and NIH Human Microbiome Project (the latter as only European partner), the FP7-MetaCardis. H2020-AD-GUT, H2020-aSynProtec and H2020-SYSCID projects. Jeroen Raes coordinates the Flemish Gut Flora project, a large scale microbiome-focused population cohort in Belgium, as well as the FWO-EOS MiQuant collaborative project. In addition, his lab is performing multiple disease-related projects in a.o. IBD, IBS, PSC, CRC, depression, PD/AD and MS on national (FWO/IWT) funding and develops novel approaches and tools for microbiome research. Key lab equipment includes the AutoMap high-throughput (192 samples/day) automated DNA extraction and sequencing library preparation platform (Hercules funding; sequencing outsourced to KU Leuven/VIB core facilities), an Accuri C6 flow cytometer (KU Leuven CREA funding), and an A35 and an A135 HEPA anaerobic workstation. In addition, the lab has automated fermentation platform operating under anaerobic conditions allowing high-throughput parallelization of milliliter-scale fermentations.
Abstract
Quantitative Microbiome Profiling in Health and Disease
Alterations in the gut microbiota have been linked to various pathologies, ranging from inflammatory bowel disease and diabetes to cancer. Although large numbers of clinical studies aiming at microbiome-based disease markers are currently being performed, our basic knowledge about the normal variability of the human intestinal microbiota and its determining factors remains limited. Here, I will discuss our findings studying a large-scale study (Flemish Gut Flora Project; n=3400) of the gut microbiome variation in a geographically confined region (Flanders, Belgium), in which analysis of microbiome variability in health identified the primary parameters associated to microbiome composition. In this presentation, I will discuss our experiences in large-scale microbiome monitoring, show how the development of dedicated computational approaches can assist in microbiome analysis and interpretation, and which confounders are essential for inclusion in microbiome disease research. In addition I will show how Quantitative Microbiome Profiling (QMP; Vandeputte et al. Nature 2017), which combines microbiomics with flow cytometry-based cell counts, is profoundly changing our view on gut microbiota variation and allowed the identification of an inflammation-associated, cross-disease enterotype.