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MRC DiMeN Doctoral Training Partnership: Characterising Human Milk Oligosaccharides in Breast Milk and their Degradation by Bifidobacterium species.

   MRC DiMeN Doctoral Training Partnership

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  Dr F Cuskin, Dr C Stewart  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

This project in collaboration with industrial partners at ThermoFisher Scientific will combine modern molecular microbiology techniques including anaerobic culturing, with protein biochemistry and carbohydrate structural analysis for a complete analysis of human milk (HMO) oligosaccharides degrading apparatus of Bifidobacterium strains and HMO profiling in breast milk samples. The student will utilise state of the art facilities newly installed at Newcastle University for the characterisation of carbohydrates by Ion chromatography-Mass Spectrometry (IC-MS). The project will include an industrial placement with ThermoFisher Scientific , world leaders in IC-MS technology, to develop methods and new technologies for HMO characterisation by IC-MS.

Necrotising enterocolitis (NEC) is intestinal disease associated with preterm infants and a cause of death. Recent research has identified links between human breast milk more specifically human milk oligosaccharides (HMOs) and the risk of developing NEC. HMOs are a driver of the infant gut microbiome and support the growth of probiotic bacteria which are associated with a healthy gut and lower incidence of NEC. Analysis of human breast milk and infant stool samples have identified specific HMOs and Bifidobacterium strains that are associated with healthy preterm infants and are in lower abundance in infants who develop NEC.  This project aims to

1.          Identify and characterise the HMO degrading apparatus in Bifidobacterium strains isolated from healthy preterm infant stools.

2.          Using Ion chromatography- Mass spectrometry profile the HMOs in human breast milk samples as a predictor of NEC.

The student will be trained in a range of experimental methods including but not limited to anaerobic microbiology, molecular biology, enzymology, mass-spectrometry analysis. This will be combined with computational methods for protein analysis through sequence analysis, phylogenetics and structural modelling. The student will also be trained in ion-chromatography-mass spectrometry and the analysis and interpretation of the data. This studentship aims to train a modern multi-disciplinary scientist who is competent in a range of computational and experimental techniques required for a microbial biochemist.

The student will be based at Newcastle University under the primary supervision of Dr Fiona Cuskin. The student will be part of a wider community of researchers with interests in the human gut microbiome, carbohydrate analysis and enzymology that crosses both the faculties of Science Agriculture and Engineering (SAGE) and Medical Sciences (FMS).

Twitter: @Fi_cuskin and @CJStewart7

Benefits of being in the DiMeN DTP:

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle, York and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here:

Further information on the programme and how to apply can be found on our website:

Funding Notes

Fully funded by the MRC for 4yrs, including a minimum of 3 months working with an industry partner.

Funding will cover tuition fees and an enhanced stipend (around £20,168). We also aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of full studentships to international applicants. Please read additional guidance here:
Studentships commence: 1st October 2023
Good luck!


Beck, L.C., Masi, A.C., Young, G.R. et al. Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants. Nat Microbiol 7, 1525–1535 (2022).
Masi AC, Embleton ND, Lamb CA, Young G, Granger CL, Najera J, Smith DP, Hoffman KL, Petrosino JF, Bode L, Berrington JE, Stewart CJ. Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis. Gut. 2021 Dec;70(12):2273-2282. doi: 10.1136/gutjnl-2020-322771
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