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MRC DiMeN Doctoral Training Partnership: Determining the influence of diet and the gut microbiome in preterm infant health and disease

MRC DiMeN Doctoral Training Partnership

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Dr C Stewart , Dr C Lamb No more applications being accepted Competition Funded PhD Project (Students Worldwide)
Newcastle United Kingdom Bioinformatics Data Analysis Immunology Microbiology Molecular Biology Food Sciences Medicine

About the Project

Preterm infants born <32 weeks gestation are ‘immature’ physiologically, anatomically and immunologically. Around 10% will develop necrotising enterocolitis (NEC), an inflammatory mediated bowel disease and 20% will develop late onset sepsis. Abnormal gut microbiome development and diet are integral to pathogenesis of both diseases.

Breast milk contains a range of components that can modulate microbiome development, including an abundance of human milk oligosaccharides (HMOs), which can act as growth substrates for probiotic bacteria.

The project will be based on preterm infant health and disease, but within this area there is flexibility in what the student can focus on, which can be modified as the project progresses. Some key objectives are likely to include:
1) Investigate the influence of maternal milk or donor milk on the preterm gut microbiome and risk of developing NEC and/or late onset sepsis

2) Experimentally test how mothers own milk, donor human breast milk, and preterm formula impact host function using a tissue-derived organoid model that recapitulates the preterm gut epithelium

3) Determine if novel therapeutics can modulate the preterm gut microbiome and host function toward a state associated with health

The student will work closely with academic and clinical supervisors and will have access to the Great North Neonatal Biobank, containing >10,000 breast milk and >30,000 preterm stool samples. They will perform metagenomic sequencing to longitudinally profile the microbiome in these important samples, alongside directly microbiological culture of bacterial isolates. The student will also establish preterm tissue-derived organoids (i.e., enteroids) from resected tissue, and use these to test how the different dietary components impact host function at the epithelial surface under a physiologically relevant oxygen gradient. This will include co-culture of donor milk, formula, and breast milk, as well as specific components including HMOs and bacterial species previously isolated.
The clinically focused work incorporates both discovery and translational aspects. During the course of this interdisciplinary project, the student will gain a wide range of relevant experience in wet-lab techniques such as microbiology, molecular biology, tissue culture, transcriptomics (host), metatranscriptomics (bacteria), alongside computational skills including the bioinformatic and statistical analysis of large multi-omic datasets.
Interested students are encouraged to contact the main supervisor, Dr Christopher Stewart - [Email Address Removed].

Find out more about the wider group and the supervisor team:

Newcastle Neonatal Nutricion and NEC (N4) Research Group

Christopher Stewart

Christopher Lamb

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 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

Studentships are funded by the Medical Research Council (MRC) for 3.5yrs. Funding will cover UK tuition fees and stipend only. We aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of bursaries that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme. Please read additional guidance here:

Studentships commence: 1st October 2021

Good luck!


1. Masi AC, Embleton ND, Lamb CA, Young G, Granger CL, Najera JA, 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. 2020. Accepted; In press.

2. Stewart CJ, Ajami NJ, O’Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni D, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She J, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF. Temporal Development of the Gut Microbiome in Early Childhood from the TEDDY study. Nature. 2018; 562. 583–588.

3. Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Nelson A, Abdulkadir B, Skeath T, Petrosino JF, Perry JD, Berrington JE, Cummings SP. (2016) Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease. Microbiome. 2016; 4(1):67
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