Term: Definition
Alpha diversity: The diversity within a community
Beta diversity: The level of similarity between communities from different hosts
Gamma diversity: The collective diversity among a collection of hosts
Operational Taxonomic Unit (OTU): Groups to which sequencing reads (i.e., 16S rRNA) are assigned based on their similarity; A representative unit of microbial sequence variation
Amplicon Sequence Variant (ASV): Inferred exact sequence (i.e., 16S rRNA) that can be used to classify members when assessing a community. A newer method that preserves sequence information and can offer higher resolution as well as consistency across studies
Carbohydrate-Active Enzyme (CAZyme): Enzymes and proteins involved in recognition, metabolism, and synthesis of complex carbohydrates (http://www.cazy.org/)
Short Chain Fatty Acid (SCFA): Volatile fatty acids with less than six carbon atoms that are the result of microbial fermentation of complex carbohydrates (i.e. formate, acetate, propionate, butyrate)
Microbial-Accessible Carbohydrate (MAC): A carbohydrate, often structurally complex, unable to be degraded/absorbed during typical mammalian digestion, can be degraded by intestinal bacteria as an energy source with resultant SCFA production (i.e., inulin)
Host-Accessible Carbohydrate (HAC) : A structurally simple carbohydrate degraded by mammalian enzymes and absorbed in the small intestine (i.e., glucose, sucrose)
Fluorescent In-Situ Hybridization (FISH): An imaging based technique using molecular probes, that can be bacteria-specific, to examine bacterial localization in a given tissue
Germ-free/Gnotobiotic: An animal devoid of known microbes (germ-free) and with a known/defined community (gnotobiotic), most commonly mice, that serve as critical tools to elucidate mechanisms of host-microbe interactions
Volatile and/or Associated Negatively with Industrialized Societies of Humans (VANISH) taxa: Taxa of bacteria that are found in non-industrialized settings, but lost or reduced in abundance in industrialized humans