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MRC DiMeN Doctoral Training Partnership: Investigating microbiome–host interactions in the preterm gut using metagenomics and stem-cell derived enteroid “mini guts”

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  • Full or part time
    Dr C Stewart
    Dr J Kirby
    Dr C Lamb
  • 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

Preterm infants born <32 weeks gestation represent a unique population and are extremely vulnerable to sepsis and/or necrotising enterocolitis (NEC; inflammatory condition of the gut), with 30% of preterm infants developing one of these diseases. Leakiness of the intestinal epithelial barrier and immaturity of the intestinal epithelial immune response are implicated as key contributory factors. Furthermore, association-based studies have demonstrated that the gut microbiome (i.e., collection of microorganisms and their function) has important links to preterm health and disease. Specifically, recent evidence from our group suggests certain bacteria, such as Bifidobacterium, may increase maturation of mucosal immunity and provide protection from the onset of these diseases.

This project seeks to extensively characterise the preterm gut microbiome and to subsequently investigate how bacteria and preterm gut epithelial cells interact. This holds exciting possibilities to better predict, diagnose, and treat infants at risk of disease. This will be achieved through the following objectives:

1) Carry out metagenomic sequencing and bacterial isolation of stool from preterm infants and maternal breast milk.
2) Perform ex vivo co-culture of dominant preterm bacteria interact with intestinal epithelial cells, utilizing human enteroids (“mini guts”) derived from patient stem cells.
3) Systematically explore how the different bacterial isolates and more holistic samples (e.g., breast milk) influence epithelial integrity and functioning. This will be determined using a wide range of cutting edge approaches including trans-epithelial electrical resistance, RNA-sequencing, quantitative PCR, metabolomics, mass cytometry, and microscopy.

This multi-disciplinary project combines wet-lab and computational elements based on state-of-the-art technologies. The clinically focused work incorporates both discovery and translational aspects.

The student will receive extensive training in metagenomic and transcriptomic sequencing, microbiology, metabolomics, tissue culture, stem cells, ex vivo modeling, cellular imaging, bioinformatics, statistics, and analytical techniques.

Additional links
Dr Christopher Stewart –
Prof John Kirby –
Dr Christopher Lamb -
Clinical website -

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 can be found on our website:

Funding Notes

Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs
Stipend at national UKRI standard rate
Tuition fees
Research training and support grant (RTSG)
Travel allowance
Studentships commence: 1st October 2019.

To qualify, you must be a UK or EU citizen who has been resident in the UK/EU for 3 years prior to commencement. Applicants must have obtained, or be about to obtain, at least a 2.1 honours degree (or equivalent) in a relevant subject. All applications are scored blindly based on merit. Please read additional guidance here:
Good luck.


1. 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 (2018) Temporal Development of the Gut Microbiome in Early Childhood from the TEDDY study. Nature. 562. 583–588.

2. Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Nelson A, Abdulkadir B, Skeath T, Petrosino JF, Perry JD, Berrington JE, Cummings SP. (2017) Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. Microbiome. 5(1):75

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. 29;4(1):67

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