Microbiome

A microbiome is the whole community of microorganisms living in a particular environment, together with their genetic material. In people, the word usually refers to the bacteria, archaea, fungi and viruses that live on the skin and in the mouth, nose, gut and vagina, and each body site has its own typical mix. Strictly, microbiota means the organisms themselves and microbiome adds their genes, although the two words are often used interchangeably.

Most resident microbes are harmless or helpful. Gut bacteria break down plant polysaccharides that human enzymes cannot digest, and some supply vitamin K. Resident microbes also occupy space and use nutrients that pathogens might otherwise take, and they help the developing immune system mature. A microbiome changes with diet, age, medicines and other exposures. Antibiotics in particular can disturb it, sometimes letting harmful organisms such as Clostridioides difficile take hold.

Because most of these microbes cannot be grown in culture, researchers study them by sequencing DNA taken directly from samples, an approach called metagenomics. The Human Microbiome Project, launched by the US National Institutes of Health in 2008, catalogued the microbes found at several body sites in healthy volunteers.