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Tens of trillions of micro-organisms, primarily bacteria, reside in the human body and collectively constitute the 'human microbiome'. Recent advances in metagenomics, metabolomics and other high-throughput, high-resolution technologies are enabling rapid progress to be made in our understanding of the fundamental role of the microbiome in human health and disease. This Collection aims to bring together original research in this expanding field and welcomes submissions on all aspects of human host-microbiome interactions.