Marie Skłodowska Curie (MSCA) Individual Fellowships 2018 Recruitment Information
Principal Investigator: Dr Brian Jones
Department: Biology and Biochemistry
Link to research webpage: Under construction – not yet available
Short description of research area to investigate with a potential MC Fellow
(Please keep within this page):
Application of viral ecogenomics to microbial source tracking.
The contamination of environmental waters used for drinking and recreational purposes with faecal pollution poses a major risk to public health. Existing methods for determining water quality based on the detection and enumeration of culturable faecal indicator bacteria (FIB) take up to 48hrs and fail to provide a reliable indication of the source of contamination. There is also increasing evidence that the behaviour and persistence of FIB in engineered treatment systems and the environment does not reflect that of pathogenic microorganisms (especially enteric viruses). Consequently, the development of methods capable of determiningthe origin of contamination (referred to as microbial source tracking – MST) has emerged in recent years as an important solution with which to monitor water quality and minimise health risks. In particular, the detection of bacteriophage that infect members of the human gut microbiome, and are specific to this habitat, represent potentially superior targets for water quality monitoring compared to their bacterial hosts. Several studies have already demonstrated the potential to utilise gut associated bacteriophage as MST tools.
We have recently extended this concept to the development of culture-independent metagenomic approaches for MST, based on relative representation of phage encoded genes within different habitats, which we term the phage ecogenomic signatures ( Our initial studies indicate that bacteriophage genomes can support a clear habitat-related ecogenomic signature that has sufficient discriminatory power be used for development of MST tools. In silico modelling indicated that ecogenomic signatures from human gut-specific phage could be used to accurately distinguish polluted from non-polluted datasets, with high specificity and sensitivity, as well as identify those contaminated by human derived pollution specifically. We now wish to build on these initial proof-of-concept studies by developing new methods for the generation of viral metagenomes using portable sequencing platforms such as the Oxford Nanopore minION, along with algorithms to process and analyse the data generated for MST applications. This work would be conducted in conjunction with collaborators at the University of Brighton UK (Dr James Ebdon, and Dr Lesley Ogilvie) and would inform research being conducted at the Chulabhorn Research Institute in Thailand (Dr Kwanrawee Sirikanchana, and Dr PomyenYotsawat).