GUT18S · Comprehensive molecular analysis and differentiation of the eukaryotic microbiota in faecal samples from human cohorts to establish the role of intestinal eukaryotes in health and disease

Comprehensive molecular analysis and differentiation of the eukaryotic microbiota in faecal samples from human cohorts to establish the role of intestinal eukaryotes in health and disease.

It has become clear in recent years that bacteria are closely linked to human health and disease, and there is recent evidence that microbial eukaryotes are equally important. The mechanisms and causality are not yet understood, but microbiota are being extensively mapped to investigate diseases, especially those of the human gut. Moreover, microbiota manipulation has increased in popularity as more data suggest links between microbiota perturbation and intestinal (diarrhoea, irritable bowel syndrome [IBS], Clostridium difficile infection, inflammatory bowel disease[IBD]) and extraintestinal disease (metabolic syndrome, non-alcoholic fatty liver disease, diabetes, etc.). The most popular amplicon-based mapping tool is 16S rDNA-based because of the universal presence of this gene, its high taxonomic data coverage, and the fact that it enables relevant distinction between taxa. We have performed such analyses extensively ourselves but consider available tools surprisingly primitive, inaccurate and incomplete. Moreover these methods have not been properly validated clinically, nor do they present combined overviews of pro- and eukaryotes, including yeasts and parasites. The current project aimed to remedy these shortcomings. Another aim was to continue our research into the clinical and public health significance of selected intestinal parasites. We therefore developed subtle, comprehensive, and highly applicable DNA-based tools for exhaustive detection and differentiation of pro- and eukaryotic organisms in not only otherwise sterile samples (blood, cerebrospinal fluid, bronchoalveolar lavage, etc.) but also in complex patient samples such as faecal samples. The main feature is the development, implementation, and clinical validation of the BION software, which has been developed in-house at Statens Serum Institut in collaboration with Danish Genomics Institute, Aarhus. Moreover, we are currently investigating the distribution of eukaryotic intestinal communities in different cohorts with a view to identifying their role in health and disease. We have developed a highly standardised diagnostic tool of unprecedented sensitivity and resolution with high applicability. This tool can be used not only for diagnosis in clinical microbiology laboratories, but also be used in research to screen for bacterial and eukaryotic organisms and communities with a view to identifying their role in health and disease (microbiota profiling). Hence, at Department of Microbiology and Infection Control, Statens Serum Institut, we recently launched a new diagnostic service, the so-called “Microbiome” test which enables comprehensive detection and differentiation of bacteria, fungi, and parasites in patient samples. We expect the service to gain quickly in popularity and will later on be launched as a gut microbiota profiling tool useful for clinical microbiology and research. Using sensitive DNA-based tools, we have shown that common, single-celled intestinal parasites, such as Blastocystis and Dientamoeba, are common in the healthy background population and that colonisation with Blastocystis is typically chronic, lasting for up to 10 years or more. It is currently not clear, what the public health significance is of such long-lasting parasitic infections. Meanwhile, we have also shown that the prevalence of these organisms is higher in the healthy background population than in patients with functional and organic bowel diseases, such as IBS and IBD. This is evidenced by multiple, independent studies. We have also discovered that Blastocystis is associated with certain microbial communities. Analysis of data obtained by metagenomic analysis of faecal DNA has shown that Blastocystis is rare in individuals with a Bacteroides-dominated microbiota, while the parasite is common in individuals in whom the microbiota is dominated by Prevotella and Ruminococcus. We are currently trying to verify this intriguing finding. We speculate that Blastocystis is linked to high gut microbial diversity and that it may be linked to butyrate-producing bacteria. Butyrate and other short-chain fatty acids have anti-inflammatory and anti-carcinogenic effects. If these findings can be confirmed, next step is to find out whether Blastocystis selects for such organisms or whether these organisms select for Blastocystis. The data obtained so far are therefore also suggestive of the potential of single-celled intestinal parasites as biomarkers and/or predictors of human intestinal health. To this end, our data may even suggest a protective role for common, single-celled intestinal parasites that are not cleared and for which only limited immunity develops, namely Blastocystis and Dientamoeba. During this CIG-related research, the PI has published more than 60 articles and four book chapters. He currently holds an H-index of 23 (Web of Science). He was a co-organiser of the “1st International Blastocystis Conference” in Ankara in 2014. He has been invited speaker at several national and international conferences, including ASM 2014, and ECCMID 2016. Independently, he has raised more than €250,000, most of which money he used to employ a PhD student (Lee O’Brien Andersen) for a period of three years. Recently, he was successful as a co-applicant on the proposal “ParaGUT – parasites, diet, and gut health”, the budget of which is €813,845 (Danish Research Council – Technology and Production) and the proposal “SOLID” (€1,889,999.41 from European & Developing Countries Clinical Trials Partnership EDCTP). He is currently the main coordinator of the proposal “Toxoplasmosis – development and application of novel methods for source attribution (TOXOSOURCE)”, a proposal developed within the Horizon 2020 Med Vet EJP track (Call: SFS36, H2020, Co-Fund EJP “One Health: Zoonoses – Emerging Threats” with a final budget of €4.0M, including a non-EU contribution of €2.0M. Since 2012, in which year the PI was awarded the CIG and appointed senior scientist at Statens Serum Institut, the PI has been developing a blog at www.blastocystis.net, a site which has been visited 495,000 times as of September 2016. At this site he blogs about his own research pertaining to Blastocystis, other intestinal parasites, and their relation to gut microbiota and gut homeostasis. He also blogs about the research of colleagues on these topics. Since June 2014, he has been employed in the United European Gastroenterology Education E-learning team, in which he regularly blogs about gut microbiota in human health and disease, and he has also been editor on the recent course on and EACME-accredited course on faecal microbiota transplantation. He has been (co-)supervising a number of BSc and MSc students over the past four years. He is currently supervising two post docs and one PhD student. He is regularly assessing MSc and PhD theses developed by candidates enrolled at the University of Copenhagen.

Data: CORDIS, © European Union