Modelling metabolic capacity and phylogeny of host and environmental niche adaptation in E. coli

MATHER_Q21DTP

The species Escherichia coli is a complex group of organisms which is found in a wide range of vertebrate animal hosts. The ability to colonise a given host is critical for E. coli and will require a different strategies, thus allowing for the evolution of separate lineages adapted to specific hosts. However, the high genetic diversity of E. coli means that detection of this niche adaptation is difficult. Given that there are multiple genotypic pathways to the same phenotypic endpoint, adaptation of E. coli to different host species may be more clearly observed by examination of phenotypes or metabolic pathways.

This multidisciplinary project will define the variation in E. coli from different host species through genomic and phenotypic analysis. A new understanding of bacterial niche adaptation and novel computational tools will be developed. This project will include both wet lab and dry lab components, including growth assays, phylogenetics, and construction of computational metabolic models. You will develop skills in state-of-the-art genomics, bioinformatics, microbiology, and computational biology.

You will join an interdisciplinary team that will support your training and development. Quadram Institute Bioscience provides a stimulating and supportive environment for research on bacterial genomics, microbiology, and the microbiome, and you will also work with One Health researchers at the Royal Veterinary College. You will have intellectual input into shaping the project and there will be opportunities to collaborate with partners both within and outside the institute to develop further skills and impact of the project.

References:

de Oliveira Martins, L., et al., Taxonomic resolution of the ribosomal RNA operon in bacteria: Implications for its use with long-read sequencing. 2020. 2: p. doi: 10.1093/nargab/lqz016.

Mather, A.E., et al., New variant of multidrug-resistant Salmonella enterica serovar Typhimurium associated with invasive disease in immunocompromised patients in Vietnam. MBio, 2018. 9(5).

Seif, Y., et al., Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nat Commun, 2018. 9(1): p. 3771.