Biomarker Discovery for Microbiome-related Diseases

PRESENTER DETAILS: 

Dragana Gagic (Moderator)
Senior Lecturer in Microbiology, Massey University, Palmerston North, New Zealand

Dragana Gagic is a senior lecturer in microbiology at Massey University, New Zealand. Her work focuses on host-microbial interactions, ranging from beneficial to pathogenic bacteria, and development and use of phage display technologies to identify molecular mechanisms mediating these interactions. More recently her research in host-microbial interactions has been redirected towards interspecies interactions between members of complex consortia, such as in animal gut, rhizosphere, fermented dairy products and flower/nectar. Another area of her research focuses on drastically underrepresented or “rare” phylotypes in the human and animal gut that could be a novel source of bioactives or keystone species.

Nur A. Hasan, PhD, MBA
CEO, EzBiome Inc.

Dr. Hasan is a molecular microbiologist with an extensive background and experience in microbiome research, bioinformatics, microbial genomics, and molecular ecology. He is an accomplished executive with experience in the strategic development of technology innovation in the biotech and life science industries. In his multidisciplinary research experience, Dr. Hasan led various genomic and metagenomic research projects in the field of infectious communicable and non-communicable diseases, microbiome, molecular ecology, and biomarker discovery that resulted in few patents and hundreds of peer-reviewed articles, abstracts, and conference proceedings. Dr. Hasan professionally serves on various prestigious scientific panels nationally and internationally, and at the Editorial Board of multiple peer-reviewed scientific journals. Currently, Dr. Hasan directs the strategic leadership and scientific functions of EzBiome Inc., a microbiome company that applies a precision taxonomy discovery platform to shorten the time for discovery and development of companion diagnostics and therapeutics biomarkers for microbiome-related diseases.

Liping Zhao
Professor, Eveleigh-Fenton Chair of Applied Microbiology, Institute for Food, Nutrition and Health, Rutgers, The State University of New Jersey, USA

Liping Zhao is currently the Eveleigh-Fenton Chair of Applied Microbiology at Department of Biochemistry and Microbiology, director for Center for Microbiome, Nutrition and Health at IFNH, School of Environmental and Biological Sciences, Rutgers University. He is a fellow of American Academy of Microbiology, a senior fellow of Canadian Institute for Advanced Research (CIFAR) and serves on the Scientific Advisory Board for the Center for Microbiome Research and Education of American Gastroenterology Association (AGA). His team has pioneered the approach of applying metagenomics-metabolomics integrated tools and dietary intervention for systems understanding and predictive manipulation of gut microbiota to improve human metabolic health. Following the logic of Koch’s postulates, Liping has found that an endotoxin-producing opportunistic pathogen isolated from an obese human gut can induce obesity in germfree mice. Their clinical trials published in Science and EBioMedicine showed that dietary modulation of gut microbiota can significantly alleviate metabolic diseases including a genetic form of obesity in children and type 2 diabetes in adults. Science magazine featured a story on how he combines traditional Chinese medicine and gut microbiota study to understand and fight obesity.

Presentation Title: Reference-free and Ecology-based Discovery of Microbiome Biomarkers
Presentation Abstract: Gut microbiome is not the “-ome of all microbial genes” but the “biome of all microbes” living in the human gut. As a microbial ecosystem, microbiome is a complex adaptive system in which strains, as the most basic building blocks, organize themselves into a higher-level structure called guilds. Guilds are functional units that consist of strains with diverse taxonomic backgrounds yet work together to contribute to community level emergent functions relevant to human health. Co-abundance analysis of amplicon sequence variants (ASVs) of 16S rRNA gene or high-quality draft genomes assembled from metagenomic datasets can help identify key guilds whose ecological behavior correlates with host phenotypes. Different from taxon-based and gene-centric approaches, this strategy does not need any prior databases and can discover ecologically robust microbiome biomarkers.

Nicole Roy
Professor, University of Otago, New Zealand

Nicole Roy is a Professor in the Department of Human Nutrition at the University of Otago with research interests in nutrition and health, host-microbiome interactions, gastrointestinal physiology, and gut-brain communication. She had science leadership roles in research programmes funded by the New Zealand Ministry of Business Innovation and Employment, Riddet Institute Centre of Research Excellence, the High-Value Nutrition National Science Challenge, and New Zealand and international food industries. Professor Roy was part of the team that established the High-Value Nutrition National Science Challenge. Her current research focuses on clinical investigations of nutrition, microbe-host interactions, gastrointestinal function, and the gut-brain axis. Professor Roy is also a Principal Investigator and leading research focusing on nutrition and food structure and their effects on digestion and host-microbe interactions as part of the Riddet Institute Centre of Research Excellence.

Presentation Title: Characterisation of the faecal metabolome in functional gastrointestinal disorders
Presentation Abstract: There is limited knowledge of the biological signatures of perturbed microbial and host processes in functional gastrointestinal disorders (FGID). The faecal metabolome of participants with FGID (irritable bowel syndrome (IBS) or functional constipation (FC) or diarrhoea (FD) symptoms, identified by the Rome Criteria IV), and healthy control participants. The faecal metabolome was measured using multi-modal liquid chromatography-mass spectrometry technologies in healthy control, constipation (FC + IBS-C) and diarrhoea (FD + IBS-D)) participants. Discriminant analysis separated participants with constipation from healthy controls and those with diarrhoea from healthy controls. The metabolites important to model separation were dissimilar in most cases between constipation and diarrhoea groups. The relative abundances of lipids, particularly ceramides, diglycerides, and triglycerides, varied between groups. Upregulated or downregulated lipid pathways were evident between the constipation and diarrhoea groups. The faecal metabolome, particularly lipids, showed perturbations that may reflect processes and mechanisms underlying FGIDs.

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