Microbiota:
The community of trillions of bacteria, fungi, and other microbes that live in your body, where your gut microbiota refers to those living in your gut. 
 

Dysbiosis:
An imbalance in the gut microbiota where less beneficial species becomes more dominant compared to helpful ones. 

Metabolite:
A small molecule produced when the body or microbes break down food or chemicals. 
 

Metabolism:
The body’s process of converting food into energy and building blocks. 

IPA (Indole propionic acid):
A health-supportive metabolite made by gut bacteria from tryptophan. 
 

KYN (Kynurenine):
A metabolite produced by the body from tryptophan, especially pronounced during immune stress. 

TRP (Tryptophan):

An essential amino acid found in protein-rich foods, used by the body (host) and gut microbiota to produce various metabolites that influence energy, mood balance, gut function, immune tone, and metabolic activity. 

SCFAs (Short-chain fatty acids):
Products of fiber fermentation that support gut barrier function and help regulate immune balance.

Intestinal Barrier Function:
The ability of the gut lining to act as a selective barrier, allowing nutrients to pass into the bloodstream while limiting the passage of unwanted microbial components. When barrier function is reduced, microbial signals can cross into circulation and interact with the immune system.

NF-kB:
A protein that controls the activation of certain genes involved in immune and stress responses.

AhR (Aryl hydrocarbon receptor): 
A protein that acts as a sensor for a wide range of small molecules – including those from the environment, food, gut bacteria, and the body’s own metabolism. When activated, it changes how certain genes are turned on or off, influencing detoxification, immune responses, and the health of barriers like the gut lining. The effect depends on what activates it; some signals promote inflammation, while others support balance and protection.   
 

IDO/TDO (Indolamine 2,3-dioxygenase / Tryptophan 2,3-dioxygenase):
Enzymes that control the first and rate-limiting step in breaking down tryptophan into kynurenine. IDO is widely expressed and activated by immune signals, especially in immune and epithelial tissues. TDO is primarily found in the liver and is regulated by stress hormones (like cortisol) and nutrient signals.

Tight Junctions (ZO-1, Occludin, Claudins):
Protein complexes that “seal” spaces between gut cells and help maintain barrier function.

Microbial Diversity:
The variety and balance of microbial species in the gut; generally linked with resilience and stable function.

Keystone Species:
Microbes that have an outsized impact on community structure and metabolite production. 

Indoles (Indole Derivatives):
Microbial metabolites made from tryptophan (e.g., IPA) that signal through receptors like AhR and support barrier and immune balance. 

Kynurenine Pathway:
A host-driven route of tryptophan metabolism that is upregulated during immune stress, producing metabolites such as KYN and QA.  

LPS (Lipopolysaccharide):
A component of certain bacterial cell walls that can interact with immune receptors when present in circulation. 

Immune Tone:
The baseline state of immune activity (neither over- nor under-responsive).

Redox Balance/Oxidative Stress:
Cellular balance between oxidants and antioxidants; relevant to mitochondrial function and metabolite effects.