The colon environment as a determinant of E. coli diversity

The bacterial species Escherichia coli can be subdivided into several phylo-groups or ‘subspecies’. Strains of the different phylo-groups differ in their ecological niche, life history characteristics, and propensity to cause disease. There is a variety of empirical evidence demonstrating that host diet, as well as gut morphology and dynamics, influence which phylo-groups are likely to establish in a host. Strains belonging to phylo-group B2 appear to be the most specialised of the phylo-groups and B2 strains are also the E. coli most likely to cause extra-intestinal diseases such as neonatal meningitis and urinary tract infection. Diet plays an important role in determining the physical-chemical environment of the colon, both directly and indirectly via diets effect on the microbial communities of the colon.

The basic goal of the proposed research is to determine if the phylo-group membership of E. coli strains isolated from a human host can be predicted based on data describing the physical-chemical profile of the faeces collected from the host. The results of the research may identify diets that may limit the establishment of phylo-group B2 strains in a host and thereby reduce the likelihood of the host acquiring a urinary tract infection. The results may explain the very large differences observed in the relative abundance of E. coli phylo-groups in humans living in different countries.

The research will provide the student with experience in a variety of basic microbiological techniques and familiarity with a variety of molecular techniques including primer design, PCR-screening and DNA sequencing. Experience with a range of chemical analysis techniques will also be acquired. Data analysis will involve a variety of phylogenetic and statistical methods. No previous experience with micro-organisms is required.