Touati Benoukraf, PhD,
Canada Research Chair (Tier II) in Bioinformatics for Personalised Medicine,
Assistant Professor, Faculty of Medicine, Discipline of Genetics
Memorial University

Studying the human microbiome: challenges and rewards

Department of Computer Science
Wednesday, February 13, 2019, 1:00 p.m., Room EN-1052

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Abstract

The microbiome in the human gastrointestinal and respiratory tract is composed of thousands of cells belonging to both pathogenic and commensal microbial communities of bacteria, fungi and virus. The
commensal organisms interact continuously with the host immune system, which in turn influences the ability of the body to mount an effective inflammatory response during stress, tissue injury and infection. With the recent improvements in sequencing technologies, we managed to generate a stream of data attesting the evident role microbiota play in developing complex diseases such as cancer. Of over 100 trillion microbes, the International Agency for Cancer Research (IACR) recognizes ten as being carcinogenic. These pathogens are Epstein-Barr virus, hepatitis viruses B and C, Kaposi’s sarcoma herpesvirus, human immunodeficiency virus-1, human papillomavirus, human T-cell lymphotropic virus type 1, Opisthorchis viverrini and Clonorchis sinensis, Schistosoma haematobium and Helicobacter pylori. It has been reported that these oncomicrobes are responsible for ~20% of all cancers. However, it has been clearly shown that, within a species, only specific strains are oncomicrobes. Traditional sequencing techniques based on the characterization of the small subunit ribosomal RNA (16S rRNA) can only identify microbes at the gender or species levels. By taking advantage of the recent long read sequencer technologies such as Nanopore, we aim to setup an experimental and computational framework to build the first database recording microbe strains of the Canadian population in the context of cancer. This tool will open new avenues in investigating the contribution of microbes in tumor immune response,
cancer development and drug responses.