Phages, faeces, and PromethION: using nanopore to investigate the cattle slurry virome
About Ryan Cook
Ryan completed his undergraduate degree in Microbiology at the University of Nottingham in 2018 and has since been working towards a Ph.D. as part of the Medical Research Foundation National Training Programme in AMR Research, also at the University of Nottingham. Ryan’s current studies investigate the diversity and ecological roles of bacteriophages within agricultural environments, under the supervision of Dr. Michael Jones and Dr. Andrew Millard.
Slurry is an economically important fertiliser, which is spread widely over UK crop fields. Despite its importance to agriculture, and widespread use in the environment, little is known about the microbial composition of slurry. We sequenced the cattle slurry virome over time using a combination of PromethION and Illumina sequencing. Whilst PromethION obtained more complete genomes, and Illumina obtained fewer errors, a hybrid assembly utilising both technologies uncovered more high-quality genomes than either short- or long-reads only. The hybrid approach uncovered 7,682 vOTUs, 98% of which were novel genera, and many of which may augment the virulence of veterinary pathogens.