Enigmatic bacterial sphingolipids: probing their immune regulatory roles in pathogenic and probiotic bacteria

About the Project

The bacterial outer membrane is the front-line defence against environmental stress and antibiotics. Textbooks tell us that lipopolysaccharide is the only lipid present in the bacterial membrane and is essential for its function. However, we have made an unprecedented discovery that pathogenic E. coli produces another type of lipid - sphingolipids – but their roles in the host are unknown. Sphingolipids are a class of structural and signalling components of eukaryotic cell membranes, essential for regulating the immune system. We hypothesise that E. coli sphingolipids will also play key, cross-kingdom immune regulatory roles within the host and contribute to stable colonisation. In our preliminary work, we discovered that almost all pathogenic strains of E. coli (including drug-resistant clones), as well as non-pathogenic probiotic strains, encode the genetic machinery to make sphingolipids. While the genes for sphingolipid synthesis are not required in laboratory conditions, genetic knockout of these genes lowers the bacteria’s survival in the gut, suggesting a key role in host-interaction.

In this project you will determine the host and environmental factors that signal to E. coli to produce sphingolipids, isolate and determine the structure of these key lipids, and explore the effects that they have on human immune cells. You will engineer a strain to constitutively produce sphingolipids in vitro. You will use random mutagenesis approaches to screen for specific regulators of the sphingolipid genes and multi-omics approaches, such as RNA-seq and lipidomics, to identify co-regulated genes and their final sphingolipid products. Wild type and mutant strains that you identify will be incubated with human macrophages and epithelial cells ex vivo to investigate the role sphingolipids play in the host immune response to these bacteria.

This highly interdisciplinary project benefits from close interactions with a group of UK and international collaborators and provides a unique training opportunity that integrates microbiology with biochemistry, omics approaches, and host interaction studies. The findings of this project will rewrite our understanding of the E. coli cell membrane and define how it interacts with its human host through its sphingolipids.