Table 1.

Glossary

Term	Definition
metagenomics	culture-free, genomic analysis of microbes by direct extraction and cloning of DNA from a particular ecosystem, such as the skin1–3
microbiome	original definition: the "ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space"4
	common usage: aggregate gene content within a microbial ecosystem5
16S rRNA gene	ribosomal gene conserved across bacteria with conserved regions used for PCR amplification and variable regions used for taxonomic classification6
MINE	maximal information-based nonparametric exploration
	a group of statistical methods to find and characterize associations in large datasets with many variables7
metatranscriptomics	culture-free analysis of total RNA (both mRNA and rRNA) isolated from a microbial ecosystem8

^1.References Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004;68:669-85.

^2.Riesenfeld CS, Schloss PD , Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 2004;38:525-52.

^3.Handelsman J, Rondon MR, Brady SF, Clardy J , Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 1998;5:R245-9.

^4.Lederberg J MA. 'Ome Sweet 'Omics - a genealogical treasury of words. Scientist 2001;15.

^5.A framework for human microbiome research. Nature 2012;486:215-21.

^6.Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R , Gordon JI. The human microbiome project. Nature 2007;449:804-10.

^7.Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh PJ et al. Detecting novel associations in large data sets. Science 2011;334:1518-24.

^8.Urich T, Lanzen A, Qi J, Huson DH, Schleper C , Schuster SC. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 2008;3:e2527.