The microbiome is the full collection of genes of all the microbes in a community, and the human microbiome is a counterpart to the human genome. The genes in our microbiome outnumber the genes in our genome by about 100 to 1.  We live in a mutually beneficial relationship with our microbes - we provide them with food and shelter, they protect against infections, toxic substances and generally keeps us healthy.

Many common diseases are associated with changes in the microbiota, termed dysbiosis. This dysbiosis is often driven by common commensal species e.g. for acne, eczema, chronic wounds and bacterial vaginosis. Both rare and common disorders are thought to have underlying contributions both from individual species and from alterations to the microbial community.