Short-chain fatty acid - produced by gut microbiota. SCFAs give immunomodulatory properties, cross the BBB, and regulate microglia. They are absorbed by intestinal cells, serving as energy and nutrients. SCFA producing bacteria are found in high fiber diets and help lower gut pH, making it less hospitable to potentially harmful bacteria

Probiotics - Contain live cultures/beneficial bacteria and should be incorporated regularly into one’s diet 

Prebiotics - Do not contain live cultures, serve as nourishment for microbiomes. Specific types include fructo-oligosaccharides

Vaginosis - An example of a microbial shift disease. Disease of the vagina cause by microbial dysbiosis (particularly loss of lactobacilli) that results in a fishy-smelling discharge, and can increase risk for other sexually transmitted diseases, pelvic inflammatory disease, and preterm birth and other pregnancy complications

Catabolism - The fermentation of dietary/complex carbohydrates, with Bacteroides responsible in the breakdown of polysaccharides (breakdown) 

Anabolism - The synthesis of nutrients/vitamins, including Vitamin B (building up)

Dysbiosis - a perturbation or imbalanced composition of the normal microbiota that results in dysfunction, disease or other pathogenic outcome. Dysbiosis can lead to serious inflammatory and autoimmune diseases (inflammatory bowel disease and Crohn’s disease). Dysbiosis can increase susceptibility to opportunistic pathogens such as Clostridium difficile 

germ-free mice - a mouse raised in a sterile environment that has no bacteria in or on them; used for infection models of diseases. Mice raised in a germ-free environment can suffer from several health issues due to the absence of beneficial microbes that normally colonize the gut

Gnotobiosis - state in which all forms of life present within an organism can be accounted for → organism completely free or colonized with known set of microorganisms

abiotic mice -  these mice have had their bacterial microbiota nearly eradicated through antibiotic treatment

Amplicon - A set of non-overlapping DNA segments that have been amplified

Contig - A set of overlapping DNA segments that are reconstructed into a single DNA sequence.

Node - a taxonomic unit on a phylogenetic tree

Branch - defines the relationship between the taxa in terms of descent and ancestry. Branch length indicates the number of changes that have occurred in that branch

cDNA - complementary DNA biochemically made from RNA by reverse transcription using a reverse transcriptase enzyme. Used in transcriptomic analysis

reverse transcription - making DNA from RNA

metabolite - a substance that is produced or used during metabolism, which is the process by which the body breaks down food, drugs, chemicals, or its own tissue. The study of metabolites is metabolomics.