Table 1.

Common Terms in the Microbiome Literature

Keyword	Definition	Examples
1. Human Microbiome	The entire collection of naturally occurring bacteria, fungi, and viruses, including their DNA, that exists in the human body which are critical for normal development and health.	Bacteria locations: mouth (anaerobes); large intestine (aerobes and anaerobes); skin (predominately aerobes) Virus locations: implant into living cells mainly in the respiratory (coxsackie viruses), gastrointestinal (adenovirus), skin- penetrating, and genital routes (human papillomavirus) Fungi locations: superficial including the skin, hair, and nails (candidiasis)
2. Microbiota	Complex communities comprised of many microorganisms including bacteria, fungi, and viruses that colonize various sites in the human body.
3. Genera	The usual subdivision of a family or subfamily in the taxonomic classification of organisms, usually consisting of more than one species.	Ex: Enterobacter (genus Enterobacter) is a group of rod-shaped bacteria of the family Enterobacteriaceae, gram-negative facultative anaerobes Ex: Escherichia coli (genus Escherichia) is a gram-negative, facultative anaerobic, rod- shaped bacterium
4. Microbes	Microorganisms such as bacteria, fungi, and viruses that can perform beneficial and harmful effects.
5. Commensal Microbes	Organisms that produce positive effects for a host. Indigenous: present on body surfaces covered by epithelial cells and exposed to the external environment.	Bacteroides, Bifidobacteria, Enterobacteriaceae, Enterococcaceae Escherichia coli, Lactobacilli Neisseria (all except N. gonorrhea and N. meningitides, Staphlococci spp., Streptococci spp.
6. Pathogenic Microbes	Organisms that produce negative effects for a host. Indigenous organisms may induce disease when the host is compromised or with commensal microbe overgrowth.	Acinectobacter, Actinobacteria,Citrobacter Clostridium spp., Firmicutes, Gemella, Geobacillus, Halomonas, Klebsiella spp., Proteobacteria, Pseudomonas aeruginosa, Shewanella , Ureaplasma (commensal in sexually active women)