As most new PhD researchers do, I feel wholly unqualified to be writing about my research area. However, having spent months reading truly inspiring work and getting my head around the aims of this project I will try to explain what I am trying to do!

Since John Snow’s revelation in 1854 that cholera was caused by sewage-contaminated drinking water, improvements in drinking and bathing water quality, have led to better public health (Hagedorm et al., 2011, Harwood et al., 2014). Luckily (and through some hard work!), most UK bathing waters are of good quality, but there is always room for improvement! Unfortunately, improving the quality of bathing water is difficult. Water quality is measured by monitoring the number of specific bacteria (E. coli and Enterococci) in the water. Whilst the sources of these bacteria, such as wastewater treatment effluent, are easy to geographically locate and therefore mitigate, others sources such as agricultural run-off are much more difficult to find.

Microbial source tracking (MST) is a collective term for the relatively new and emerging techniques that try to find these sources of biological pollution entering a  (Hagedorm et al., 2011). There are a huge number of MST approaches (which are saved for a later post!); the most successful of which use biological markers or bacterial communities to identify these pollution sources. However, after almost 2 decades of research there is no consensus on the most appropriate MST approach (Hagedorm et al., 2011). This could be due to the range of potential applications of MST, making it likely that the best approach is specific to a particular problem or the difficulties in validating approaches.

Through this project we hope to take advantage of advances in next generation sequencing (NGS) technology to update current and develop new microbial source tracking (MST) methods and validate these robustly. We also aim to produce a source tracking tool to allow MST methods to be used rapidly and compared accurately.

I don’t imagine for one moment that it will be plain sailing, but I will try to document all successes and failures as best I can, post by post!


Hagedorm, C., Blanch, A. R. H. and Harwood, V. J. (2011) Microbial Source Tracking, Applications, and Case Studies. Springer: New York.

Harwood, V. J., Staley, C., Badgley, B. D., Borges, K. and Korajkic, A. (2014) Microbial source tracking markers for detection of fecal contamination in environmental waters: Relationships between pathogens and human health outcomes FEMS Microbiology Reviews, 38, 1 1-40.