Imperial College London


Faculty of MedicineDepartment of Medicine

Research Fellow



+44 (0)20 7594 2074thomas.clarke




5.40CFlowers buildingSouth Kensington Campus





Environmentally exposed surfaces in humans are colonized by a vast number of foreign microbes (the commensal microbiota) and these organisms play a key role in regulating mucosal and systemic immune function. Disruption of this relationship is linked to a wide variety of diseases and immune dysfunctions, including chronic inflammatory conditions at the mucosa, autoimmunity and increased susceptibility to infection by bacteria, viruses and parasites. There remains, however, a major gap in understanding the mechanistic basis for the influence of the commensal microbiota on immune function, especially systemic immunity. The broad theme of my research, therefore, is to understand how programming of innate immunity by the microbiota influences host responses to bacterial infection and vaccination, and how changes to the composition of the microbiota disrupts these responses.



McDonald JAK, Mullish BH, Pechlivanis A, et al., 2018, Inhibiting Growth of Clostridioides difficile by Restoring Valerate, Produced by the Intestinal Microbiota., Gastroenterology

Glanville DG, Han L, Maule AF, et al., 2018, RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization, Plos Pathogens, Vol:14, ISSN:1553-7366

Dominguez-Huettinger E, Boon NJ, Clarke TB, et al., 2017, Mathematical Modeling of Streptococcus pneumoniae Colonization, Invasive Infection and Treatment, Frontiers in Physiology, Vol:8, ISSN:1664-042X

Brown RL, Sequeira RP, Clarke TB, 2017, The microbiota protects against respiratory infection via GM-CSF signaling, Nature Communications, Vol:8, ISSN:2041-1723


McDonald JAK, Mullish BH, Pechlivanis A, et al., 0503 - A novel route for controlling Clostridioides difficile growth via bile acid and short chain fatty acid modulation, ISME17

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