Innate immune cells – and many other cells – express evolutionarily conserved, germline-encoded receptors that recognize seemingly pathogen-derived ligands (also termed pathogen-associated molecular patterns), thereby allowing the host to perceive infection. Although they were the first to be discovered, Toll-like receptors (TLRs) are not the only pattern recognition receptors. TLRs are unlikely to discriminate between commensals and pathogens in the gut microbiota. There is, however, increasing evidence that TLRs shape intestinal function. In addition, certain bacteria appear to drive either Th1/Th17 proinflammatory immune responses, or T regulatory responses. Furthermore, TLRs appear to trigger ‘sterile’ autoinflammatory responses by sensing metabolically altered host (self) components.

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