Diversity of Escherichia coli along the intestinal tract

The community of bacteria present in the human gut is an important determinant of human health. There has been a wealth of recent studies examining the factors that determine the diversity of the human microbiome and explore the nature of the interactions occurring between the host and its microbiome. Such studies are usually based on bacteria isolated from biopsy samples or from faecal material. While it is recognised that the mucosal associated microbial community differs from that of the lumen, there is some data to suggest that bacteria present in the gut may not be detected in faecal samples. Thus the extent to which faecal samples are a true representation of the gut microbiome is unknown.

The goals of this study are two-fold. One, to determine the extent to which the faecal microbiome differs from that of the gut and two, add to the body of knowledge concerning the genetic structure of bacteria isolated from different regions of the gut.

The study will involve the isolation of bacteria from faeces and various gut regions of rats. The project will provide the student with experience in basic microbiological techniques, including the isolation and enumeration of E. coli. The student will also gain experience with PCR-based fingerprint analysis of E. coli, phylo-typing, and virulence gene screening, as well as the analysis of such data. The study will also include characterising gut and faecal 16S metagenomic microbiome analysis using a high throughput sequencing technique, as well as the statistical analysis of metagenomic data. No previous experience with micro-ogranisms is required. The project is suitable for either a February or July start.