Philip Hugenholtz is a microbiologist who has made landmark contributions in the field of culture-independent analysis of micro-organisms. He discovered and characterised numerous previously unrecognised major bacterial and archaea lineages each with greater evolutionary divergence than animals and plants combined. He has been instrumental in the development and application of metagenomics, the genome-based characterisation of microbiomes, which has revolutionised our understanding of microbial ecology and evolution. His contributions have raised awareness of the human microbiome and its role in health and disease.