The human microbiome and host-pathogen interactions

Abstract

In the past, medical microbiology has largely relied on simplifying assumptions of one-to-one relationships: between a single pathogen and a single disease or between a single gene and virulence-related phenotype. Now, thanks to technical and conceptual advances, we are moving towards a new paradigm, in which pathogen-host interactions are best evaluated against the backdrop of the complex community of germs, genes and genomes known as the human microbiome, which acts as a reservoir of colonisation, virulence and resistance determinants. This new outlook blurs the boundaries between pathogen and commensal, emphasises the immunological crosstalk between microbiota and host and recognises the complex interplay between the human microbiome, colonisation resistance, diet, antibiotics and inflammation. On this view, pathogenesis is more like guerrilla warfare or terrorism than a clash between standing armies - the success of the pathogen, like that of the partisan, depending critically on what is happening in the local community.