Controlling Clostridioides difficile infections through modulation of gut bile acids

Gut bile acids (BAs) play a central role in human health. Synthesised in the liver, primary BAs are subsequently modified by the gut microbiome into secondary BAs of increased diversity and function which can control the emergence of dangerous pathogens such as Clostridioides difficile, the leading cause of antibiotic associated diarrhea in humans. Transmission of C. difficille is via the ingestion of spores which require certain primary BAs in order to germinate into the vegetative cells that multiply and produce the disease-causing exotoxins, TcdA and TcdB.  In contrast, secondary BAs inhibit spore germination.  Moreover, they also inhibit C. difficile vegetative growth and toxin activity as well as modulating host immune and inflammatory responses. Controlling gut BA composition, therefore, represents an effective strategy of controlling C. difficile infections (Cdi).

Several bacteria of the microbiota have been identified as being important in converting primary to secondary BAs, most notably Clostridium scindens and Clostridium hiranonis, both of which carry a bile acid-induced operon (termed bai) encoding the enzymes presumed responsible. In essence, organisms such as C. scindens are responsible for colonization resistance – the inability of C. difficile to colonise a healthy microbiome.  Despite the strong evidence that supports this hypothesis, definitive proof through the implementation of Molecular Koch’s postulates has yet to be derived. Thus, to date, it has not proven possible to generate mutants of either C. scindens or C. hiranonis in which the gene(s) encoding the pivotal enzymes responsible for bile acids conversion have been inactivated and thence complemented.  Fortunately, SBRC Nottingham have now demonstrated gene transfer in both species and recently generate a bai mutant in C. hiranonis using RiboCas.

The PhD’s goal is to capitalize on these breakthroughs and use engineering biology to create microbes that can modulate the composition of bile acids in the gut as a means of preventing Cdi.  We will place those genes pivotal to BA conversion under the control of inducible promoter systems in microbiome-associated bacteria that either: (i) carry a native bile acid-converting pathway (primarily C. scindens and C. hiranonis), or; are a surrogate (Clostridium butyricum) into which the pathway is chromosomally inserted.  At the same time we will make the strains conditional for sporulation, thereby controlling their release to the environment.  The project will involve anaerobic microbiology, DNA synthesis, cloning, synthetic biology, CRISPR/Cas genome editing, electron/high resolution microscopy, bioinformatics, in vivo testing, receptor biology, therapeutics and biochemistry.

This is a collaboration between the School of Science and Technology at Nottingham Trent University and the Synthetic Biology Research Centre (SBRC) at the University of Nottingham, and forms part of the multimillion-pound NIHR-funded Biomedical Research Centre (BRC) housed in the Queens Medical Centre.

Supervisory Team:

Dr Sarah Kuehne (Director of study, NTU)

Prof Nigel Minton (second supervisor, UoN)

Dr Klaus Winzer (third supervisor, UoN)

Dr Tanya Monaghan (Fouth supervisor, Associate prof and honorary Consultant in Gastroenterology, UoN/BRC)

References

Cañadas IC, Groothuis D, Zygouropoulou M, Rodrigues R, Minton NP. RiboCas: A Universal CRISPR-Based Editing Tool for Clostridium. ACS Synth Biol. 2019; 8(6):1379-1390. https://doi.org/10.1021/acssynbio.9b00075

Studer N, Desharnais L, Beutler M, Brugiroux S, Terrazos MA, Menin L, Schürch CM, McCoy KD, Kuehne SA, Minton NP, Stecher B, Bernier-Latmani R, Hapfelmeier S. Functional Intestinal Bile Acid 7α-Dehydroxylation by Clostridium scindens Associated with Protection from Clostridium difficile Infection in a Gnotobiotic Mouse Model. Front Cell Infect Microbiol. 2016; 6:191. https://doi.org/10.3389/fcimb.2016.00191

Entry qualifications

At least a 2.1 Honours degree in Microbiology, Biochemistry or a related field.

Informal inquiries can be made to [email protected]

Fees and funding

The three-year studentship covers tuition fees and a tax-free stipend, UK Students only.