Table 1.

Glossary

Metagenomics. A rapidly evolving field that emerged from rapid advances in DNA sequencing methods, with a focus on the use of culture-independent methods to study the structures, functions and dynamic operations of microbial communities. Frequently used to refer to the technique of isolating and sequencing community DNA directly from an environment, but extends to the profiling of gene expression at the level of RNA (metatranscriptomics), and protein (metaproteomics), as well as community metabolism (metabolomics).

Microbiota. A microbial community; commonly referred to according to the habitat that it occupies (e.g. the gut microbiota).

Microbiome. The aggregate genomes and genes found in the members of a microbiota.

Phylotype (or operational taxonomic unit, OTU). A group of microbes, commonly defined by the level of sequence similarity (percentage identity) between small subunit (16S) rRNA genes (e.g. ≥ 97% for a ‘species’-level phylotype).

‘Core’ human gut microbiome. A set of features shared across all or the vast majority of gut microbiomes (e.g. genes and/or metabolic capabilities).