Department Seminar Series - David Werner, Ph.D

We describe the technical feasibility of bacterial community characterization via analysis of environmental DNA, using only portable equipment items. To this end we assembled a suitcase laboratory which includes the memory-stick sized MinION sequencing device of Oxford Nanopore Technologies, a light-weight qPCR instrument from Quantabio, and all the equipment items needed for the biomass concentration, DNA extraction, purification, quantification, gene amplification, and sequencing library preparation. At a sewage treatment plant in the UK, and at the Addis Ababa Water and Sewerage Authority in Ethiopia, the 16S rRNA gene sequencing workflow, including DNA extraction, PCR amplification, library preparation, and sequencing, was accomplished within one working day. The taxonomic data became available within 24–72 h, depending on internet speed. We also deployed the suitcase laboratory in the back of a van for faecal pollution source tracking in the UK with onsite qPCR assays that can quantify marker genes for human-host associated Bacteroides within 4 hours of sampling. Our field deployable toolbox advances the capability of scientists to comprehensively monitor microbiomes and associated hazards anywhere in the world.

Dr. David Werner is a professor of environmental systems modelling at Newcastle University, UK. He earned his PhD in Environmental Sciences at EPFL in Switzerland. His research group works towards ubiquitous genomics in water, sanitation, and hygiene (WASH) to achieve the United Nation’s Sustainable Development Goal 6: Clean water and sanitation for all. This includes the co-development and testing of a suitcase laboratory for molecular microbiology with colleagues in Africa, South America, and South Asia. David enjoys doing fieldwork with his colleagues and students, and life-long learning about the wonders of nature and human follies.