Characterising Human Milk Oligosaccharides in Breast Milk and their Degradation by Bifidobacterium species

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.