Table 1.

Key terms.

Gnotobiotics	Derived from the Greek roots gnostos ‘known’ and bios ‘life’; refers to animals that are maintained without exposure to microbes (germ-free) prior to microbial colonization. Frequently used study groups include mono-or bi-association (1–2 microorganisms), conventionally-raised (maintained outside an isolator in a standard mouse facility), conventionalized (i.e., ex-germ-free; colonized with a complex microbiota), or humanized (colonized with a human sample).
Metagenomics	A rapidly growing field that focuses on using culture-independent techniques to characterize the structure and function of microbial communities and their interactions with the environment. Metagenomic studies include (i) shotgun sequencing of microbial DNA isolated directly from a given environment, (ii) high-throughput screening of expression libraries, constructed from cloned community DNA (functional metagenomics), (iii) profiling of community-wide gene expression and protein abundance (meta-transcriptomics and meta-proteomics), and (iv) identification of a community’s metabolic network (metabolomics).
Microbiota	A microbial community, often including Bacteria, Archaea, small Eukaryotes, and viruses occupying a given habitat.
Microbiome	A term used to refer to the aggregate genomes present in members of a given microbiota, and the activities that they encode.
Xenobiotics	Compounds foreign to a living organism, used here to refer to therapeutic drugs, antibiotics, and diet-derived bioactive compounds.