Dr Lindsay Hall

Group Leader

Contact via email

Early life microbiota-host interactions


I qualified with a BSc (Hons) in Microbiology from the University of Glasgow in 2003. I then went on to study for a PhD in Microbiology and Immunology at the Wellcome Trust Sanger Institute (University of Cambridge) under the supervision of Prof Gordon Dougan.

My thesis focused on designing and creating mucosal vaccines against Mycobacterium tuberculosis and characterising mucosal immune responses (specifically Natural Killer, [NK] cells) induced after oral and intranasal immunisations. My PhD was part funded through the EU sixth framework programme entitled Mucosal Vaccines Against Poverty Related Diseases (MUVAPRED).

In 2007 I took up a postdoctoral position at the APC Microbiome Institute, University College Cork in Ireland. During my time in Cork, I moved into a new mucosal immunology area focused on intestinal inflammatory disorders. My research utilised experimental Ulcerative colitis and enteric pathogen models to understand the protective role of early mucosal immune responses (including NK cells) during acute intestinal inflammation. In Cork, I also started to work on the bacterial communities that inhabit the gut, termed the microbiota, specifically understanding the role of individual members (i.e. Bifidobacterium) and their products (exopolysaccharide capsules) in modulating the critical commensal-host interaction.

I returned to the UK in 2011 to take up a lecturing and Principle Investigator position within the Norwich Medical School, University of East Anglia.  In 2013 I was awarded a Wellcome Trust Investigator Award to study the role of early life gut microbiota in colonisation resistance development and was promoted to senior lecturer in 2014. In 2015 I moved to the Institute of Food Research as the Microbiome Group Leader and my team studies the early life microbiota in health and disease.

Key publications

Hughes KR, Harnisch L, Alcon-Giner C, Mitra S, Wright CJ, Ketskemety J, van Sinderen D, Watson AJM, and Hall LJ. Bifidobacterium breve reduces apoptotic epithelial cell shedding in an exopolysaccharide and MyD88-dependent manner. Open Biology. 2017. DOI: 10.1098/rsob.160155

Hall LJ, Murphy CT, Quinlan A, Hurley G, Shanahan F, Nally K, Melgar S. Natural killer cells protect mice from DSS-induced colitis by regulating neutrophil function via the NKG2A receptor. Mucosal Immunol. 2013;6(5):1016-26

Hall LJ, Murphy CT, Quinlan A, Hurley G, Shanahan F, Nally K, Melgar S. Natural Killer cells protect against mucosal and systemic infection with the enteric pathogen Citrobacter rodentium. Infect. Immun. 2013;81(2):460-9

Hall LJ/Fanning S, Cronin M, Zomer A, MacSharry J, Goulding D, O’Connell-Motherway M, Shanahan F, Nally K, Dougan G, van Sinderen D. Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation & pathogen protection. Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2108-13.

Hall LJ/ Jansen AM, , Clare S, Goulding D, Holt KE, Grant AJ, Mastroeni P, Dougan G, Kingsley RA. A Salmonella Typhimurium-Typhi genomic chimera: A murine-typhoid model to study Vi polysaccharide capsule function. PLoS Pathogens. 2011 Jul;7(7):e1002131.

Greenhough B., Read C. J., Lorimer J., Lezaun J., McLeod C., Benezra A., Bloomfield S., Brown T., DAcquisto F., Clinch M., Dumitriu A., Evans J., Fawcett N., Fortané N., Hall L. J., Herrera C. E. G., Hodgetts T., Johnson K. V. A., Kirchhelle C., Krzywoszynska A., Lambert H., Monaghan T., Nading A., Nerlich B., Singer A., Szymanski E., Wills J. ... (2020)

Setting the agenda for social science research on the human microbiome

Palgrave Communications , 6, 18

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Hughes K. R., Schofield Z., Dalby M. J., Caim S., Chalklen L., Bernuzzi F., Alcon C., Le Gall G., Watson A. J. M., Hall L. J.. (2020)

The early life microbiota protects neonatal mice from pathological small intestinal epithelial cell shedding.

FASEB Journal

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Püngel D., Treveil A., Dalby M. J., Caim S., Colquhoun I. J., Booth C., Ketskemety J., Korcsmaros T., van Sinderen D., Lawson M. A., Hall L. J.. (2020)

Bifidobacterium breve UCC2003 Exopolysaccharide Modulates the Early Life Microbiota by Acting as a Potential Dietary Substrate.

Nutrients, 12

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Chen Y., Brook T. C., Soe C. Z., O'Neill I., Alcon C., Leelastwattanagul O., Phillips S., Caim S., Clarke P., Hall L. J., Hoyles L.. (2020)

Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors.

Microbial genomics

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Kiu R,Treveil A,Harnisch L,Caim S,Leclaire C,van Sinderen D,Korcsmaros T,Hall L. (2020)

Bifidobacterium breve UCC2003 Induces a Distinct Global Transcriptomic Program in Neonatal Murine Intestinal Epithelial Cells.

iScience, 23, 101336

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