The Microbiome of the Cam
Chasing the invisible diversity of microbial life forms in freshwater
with a portable DNA sequencer
Year by year, Cambridge rowers, swimmers and punters obtain serious infections associated with pathogens obtained from the river Cam's water. Most Cambridge citizens and visitors approach the prospect of a Cam swim with a healthy dosis of scepticism. Is this justified?
Despite the widespread doubts about the Cam’s water quality, an information and research framework that targets the potential microbial culprits is lacking. In October 2017, our team PuntSeq has launched its mission to change this state!
By utilising a small and portable real-time DNA analyzer, Oxford Nanopore’s MinION, we are monitoring the bacterial communities of nine different spots along the Cam trajectory within, upstream and downstream of Cambridge. We are using various cost-effective technologies to quantify microbial pathogens across time and space, and relate our results to local environmental parameters such as water temperature and pH.
PuntSeq was founded as a citizen science project. All of our results will be made accessible through a range of public events, online media and open-access resources.
If you like to learn more, watch our video, read about our latest sampling efforts and make sure to follow us on twitter (@puntseq).
In the water:
We take surface water samples at nine different locations along a stretch of five miles of the river Cam. Spots include popular destinations around Cambridge, such as Byron’s Pool, Grantchester Meadows, the Bridge of Sighs at St. John’s College, or Baits Bite Lock near Fen Ditton. We aim to study spatial gradients of microbial communities within the small-scale context of urban water pollution, and to assess the impact of the city of Cambridge on its many river stakeholders: punters, rowers, anglers, dog owners and houseboat residents.
In the lab:
After taking a 400 ml water sample, we measure its physical parameters (pH, temperature, turbidity and dissolved oxygen) by integrating all sensors on a custom-built Arduino Nano station. Subsequently, we isolate the water's bacterial DNA with a standardised filter extraction protocol. Our team then uses so-called “16S rRNA” bacterial DNA barcodes to obtain a genetic footprint of each sample, which is analysed with Oxford Nanopore Technologies' MinION.
In the cloud:
Our expertise in Bioinformatics allows us to efficiently process and analyse raw DNA sequencing data. We devise existing and novel workflows to combine both physical and biological information from our samples, building on reproducible data science to reliably determine the abundance of pathogens and other microbes in our river.