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.



Dominguez-Huttinger E, Boon NJ, Clarke TB, et al., Mathematical modelling of colonization, invasive infection and treatment of Streptococcus pneumoniae, Frontiers in Physiology, ISSN:1664-042X

Brown RL, Clarke TB, 2017, The regulation of host defences to infection by the microbiota, Immunology, Vol:150, ISSN:0019-2805, Pages:1-6

Hergott CB, Roche AM, Tamashiro E, et al., 2016, Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis, Blood, Vol:127, ISSN:0006-4971, Pages:2460-2471

Pader V, Hakim S, Painter KL, et al., 2016, Staphylococcus aureus inactivates daptomycin by releasing membrane phospholipids., Nat Microbiol, Vol:2

Clarke TB, 2014, Early Innate Immunity to Bacterial Infection in the Lung Is Regulated Systemically by the Commensal Microbiota via Nod-Like Receptor Ligands, Infection and Immunity, Vol:82, ISSN:0019-9567, Pages:4596-4606

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