Improving our planet’s water quality constitutes a UN Millennium Development Goal, with pathogen contamination being one of the top priority concerns. While the recognition and understanding of changing microbial communities in water resources is essential, global pathogen-level impacts of climate change and rising urbanization yet need to be studied.
PuntSeq has developed a real-time workflow for rapid and cost-effective assessments of microbial freshwater communities. We document all necessary steps, from water sampling to DNA extraction, bacterial sequencing and downstream Bioinformatics analyses.
We employ Oxford Nanopore Technologies’ MinION for DNA analysis; this small and convenient instrument has already been used for pathogen surveillance in other contexts, most famously for monitoring the 2015 outbreaks of Ebola in West Africa and Zika in Brazil. The MinION allows for real-time in situ data analysis, due to its easy transportation and user-friendly protocols. To make the most of this device’s portable nature, our ultimate goal is to design a mobile DNA sequencing workflow that enables citizens around the globe to analyse their own freshwater sources - anywhere, at any time.
PuntSeq aims at a comprehensive, transparent and easy to use metagenomic analysis of MinION data. Our bioinformatics team has assessed the performance of several taxonomic classifiers, including new tools such as Minimap2, SPINGO and BugSeq. Building on these experiences, we have developed an optimised, fully automated, open-source pipeline that enables biological insights from metagenomic sequencing. This includes the identification of well-known bacterial water contaminants. For more details, have a look at our GitHub page.
The MinION is a great tool to obtain genetic information, and to thereby provide us with an idea about the microorganisms inhabiting specific locations of our rivers. We have additionally devised a simple and cheap DIY (do-it-yourself) kit to measure environmental parameters at the same locations, to then align this information with the presence of certain organisms. Our water testing equipment is based on the open source electronic prototyping platform Arduino, and it can be used to measure water temperature, dissolved oxygen concentration, pH and turbidity.