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The innate immune system plays an important role in shaping the microbiota into configurations that are tolerated and beneficial to the host, thereby playing a crucial role in human health. Innate immunity is based on the fundamental principle that Pattern Recognition Receptors (PRRs) recognise pathogen associated molecular patterns as non-self-entities and trigger intracellular signalling pathways that lead to the induction of numerous cytokines and chemokines that help maintain host resistance to infections. Dysregulation of this interaction has been identified as the core defect that leads to chronic intestinal inflammation allowing certain microbiota to be harmful to host health. This dysbiosis of the microbiome is found associated with numerous chronic diseases. A logical explanation would be that genetic defects in the recognition and response pathways that the host uses to identify these microbial pathogens could lead to altered microbial colonisation or mis-recognition of normal bacteria leading to diseases. The interaction between pattern recognition receptors, microbial traits and human health with respect to the gut are now rapidly resolved and will be the subject of this review.

Original publication




Journal article


Best practice & research. Clinical gastroenterology

Publication Date





683 - 691


MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK; Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK; Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, UK.