Is there something that came out of the project that you never expected at the beginning?
A working DNA extraction protocol, a working MinION and a working Arduino platform!
How has the OpenPlant Fund enabled the development of the project?
Through the generous funding of the OpenPlant grant, we have been able to purchase the MinION starter kit for $1000, different water DNA extraction kits, basic lab equipment and our set of Arduino sensors and wires. Moreover, Dr Colette Matthewman and Dr Jenny Molloy from OpenPlant have kindly brought us in touch with algal expert Dr. Ben Wagstaff, helping us to establish an ideal Cambridge-Norwich collaboration which will help us immensely in expanding the applicability of our approach to algal contamination of freshwater waterways. The Fund's excellent outreach network has helped us in amplifying results and messages of our project through social media channels, mainly via twitter, in addition to their kind provision of facilities for a MinION metagenome sequencing workshop that we will hold in Cambridge very soon.
How do you feel the project is progressing?
Since our PuntSeq project received its first financial funding around half a year ago, it has progressed very quickly. In these few months, our team has been able to learn about all steps that are necessary to perform metagenomics surveillance analyses, from environmental measurements over DNA extraction and MinION sequencing to bioinformatic post-processing of the data. Hereby, it is great to see how much we have learned from each other, but also entirely from scratch by reading subject literature, talking to experts and simply by trial and error. We are now at a stage where we have optimised all individual protocols to perform a major water sampling and sequencing effort at various locations of our river Cam. We expect to be able to provide a profound overview of the microbial community of the Cam by the end of Spring.
Overall, our outreach activities have been very successful although we did not present much data yet. Both scientific and non-scientific communities have shown strong interest in our project, we received a lot of positive feedback, won multiple best-poster-prizes at conferences and motivated many people to follow our progresses via Twitter (@puntseq). We are confident that this already large interest will further increase with our first results about the river Cam being released, and we are currently strengthening our public engagement efforts, e.g. by taking part in events like “A Pint of Science”, by producing a professional movie clip and conducting an online-survey on infection rates through direct contact with the Cam.
What are the future opportunities to take this project forward?
We founded PuntSeq to inform the general public about the merits of DNA sequencing, especially about the direct impact it might have on peoples' health. In future, we would ideally like to sample from multiple rivers of the greater Cambridgeshire area and beyond, producing a map of microbial communities along the length of respective waterway trajectories. We hope to share our findings with relevant environmental authorities in Cambridge and East Anglia, and to influence environmental conservation through genomics. Our team is also further streamlining the process from extraction of the aquatic DNA to sequencing with the MinION and automatic identification of potential pathogens in the field, so that non-specialists can perform these experiments and gain a deep insight into the beautiful science of microbiology.