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Investigating the mechanism of dietary fibre breakdown by the human and animal gut microbiota

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  • Full or part time
    Dr D Bolam
    Prof D Rigden
    Dr Jon Marles-Wright
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

The gut microbiota of many mammals, including humans and farmed animals, plays a critical role in the digestion of plant polysaccharides (often called dietary fibre) from crops and the products of this anaerobic fermentation provide major health benefits to the host. It is therefore important to understand the mechanisms by which prominent members of the gut microbiota interact with and degrade food/feed to inform both nutritional strategies to benefit host health, as well as facilitate development of novel crop traits aimed at maximising their health benefits (i.e. to develop varieties that are broken down more efficiently by the gut microbiota).

This studentship is a collaboration between Dr David Bolam’s and Dr Jon Marles-Wright’s labs at Newcastle and Prof Dan Rigden’s lab at Liverpool aimed at furthering our understanding of how the gut microbiota of humans and animals interacts with and processes dietary fibre.

The student will utilise a range of cutting edge bioinformatics techniques at Liverpool and biochemical, structural and cell biology techniques at Newcastle to characterise the main glycan degrading enzymes from key gut bacteria and understand their role in plant polysaccharide breakdown in the gut. The data generated will provide significant insight into the mechanism of fibre degradation by the gut microbiota and thus underpin the development of strategies designed to improve the nutritional value of plant based foods for both humans and farmed animals.

Applications should be made by emailing [Email Address Removed] with a CV (including contact details of at least two academic (or other relevant) referees), and a covering letter – clearly stating your first choice project, and optionally 2nd and 3rd ranked projects, as well as including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project(s) and at the selected University. Applications not meeting these criteria will be rejected.
In addition to the CV and covering letter, please email a completed copy of the Additional Details Form (Word document) to [Email Address Removed]. A blank copy of this form can be found at:
Informal enquiries may be made to [Email Address Removed]

Funding Notes

This is a 4 year BBSRC studentship under the Newcastle-Liverpool-Durham DTP. The successful applicant will receive research costs, tuition fees and stipend (£15,009 for 2019-20). The PhD will start in October 2020. Applicants should have, or be expecting to receive, a 2.1 Hons degree (or equivalent) in a relevant subject. EU candidates must have been resident in the UK for 3 years in order to receive full support. Please note, there are 2 stages to the application process.


Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci. Nat Microbiol. (2019) 4:1571-1581.

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans. Proc. Natl. Acad. Sci. USA. (2017) 114:7037-7042.

Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Nature (2017) 541:407-411.

Glycan complexity dictates microbial resource allocation in the large intestine. Nat. Commun. (2015) 6:7481.

Evidence that GH115 α-glucuronidase activity, which is required to degrade plant biomass, is dependent on conformational flexibility. J. Biol. Chem. (2014) 289; 53-646.

Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. (2011) 9:e1001221.

Specificity of polysaccharide use in intestinal Bacteroides species determines diet-induced microbiota alterations. Cell (2010) 141:1241-52. First name author was a PhD student of Lead supervisor.

Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase. BMC Bioinformatics (2014) 15:196.

From Protein Structure to Function with Bioinformatics. 2nd edition. Springer, Dordrecht (2017).

Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains. Proc Natl Acad Sci USA. (2012) 109:6537-42.

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