Gut Biology Key Terms

Table of Contents

Gut Biology

GI tract structures

  • [Alimentary Canal]: Continuous tube that extends from the mouth to the anus through the thoracic and abdomen and pelvic cavities. aka Gastrointestinal Tract

  • [Salivary glands]: Initiates digestion of starches through enzymes

  • [Liver]: Regulates chemical levels in the blood and excretes a product called [Bile].

  • [Gallbladder]: Stores the excretions that the Liver and Pancreas excrete ([Bile])

  • [Pancreas]: Excretes enzymes ([Lipase], [Protease], [Amylase]) that in combination with [Bile] help break down food

  • [Stomach]

  • [Intestine] (small and large)

  • [Microvilli]: the inner wall of the lumen that absorb nutrients from the small intestine

  • [Epithelium]: a border that houses different types of cells all along the GI tract. Some including squamous and columnar epithelium, endocrine cells, and immune cells m cells.

  • [Lamina Propria]: A connective tissue containing many blood & lymphatic vessels, immune cells

Breakdown of food -> molecules

  • [Bile]: Partially responsible for emulsification and absorption of lipids. In other words, partially responsible for the digestion of fats to fatty acids.
  • [Food Bolus]: The initial mixture of food and Saliva
  • [Chyme]: The mixture of saliva, food, & gastric juices
  • Polypeptides: The broken down structure of proteins
  • Triglycerides: The broken down structure of fats – cannot be absorbed by the intestine
  • Emulsification: the process of taking substances that wouldn’t previously mix and mixing them
  • Micelles: The end result of emulsified Bile salts + monoglycerides through lipases from Fat globules so that the monoglycerides can enter the Epithelial cell layer and be absorbed

Simple sugars

Glucose Lactose Sucrose Fructose Galactose


  • [Lipase]: Combined with [Bile] from the [Liver], lipase breaks down fats into smaller and smaller molecules.

    Often people without enough lipase have vitamin deficiencies in fat soluble vitamins such as A, E, and K. Another clear sign would be fatty stools, which are overly foul smelling and float on top of the water in the toilet bowl.

  • [Protease]: These enzymes digest the protein in our diet into single amino acids. People struggling to break down protein can often have increased food sensitivities and allergies

  • [Amylase]: These enzymes are responsible for breaking down starches and carbs into simple sugars. Incomplete digestion of carbs can often lead to diarrhea, gas and bloating.

Table of Contents

  1. Microbiome


  • [Microbiome] - The genetic material of all the microbes - bacteria, fungi, protozoa and viruses - that live on and inside the human body
  • Germ-free mice - a mouse with no microbiome Antibiotics - medication that kills bacteria. This will wipe out your gut microbiome and cause issues. Obesity - There is a link between the microbiome and obesity. Often times the Asthma Diabetes Inflammatory bowel disease (IBD) [Dietary emulsifiers] - thickeners, mix things that often won’t mix. All the ‘gums.’ Disrupt the mucosal barrier Artificial sweeteners - also disrupt the mucosal barrier in your gut. Malnutrition Insulin resistance

Immune Connection

  • [Immune System] microbiome contributes to the development of the immune system immune system alters the composition of the [microbiome]
  • Pattern recognition receptors
  • Pathogen-associated molecular patterns
  • Antibodies: B cells, most importantly lgA. They bind bad bacteria and renders them useless so they just pass. Another way that the body sees bacteria
  • Dendritic cells (DCs): produce antibodies by binding bacteria that antibodies will be created to fight
  • Lymph Nodes: Places where B cells live. B Cells generate lgA
  • Immunoglobulin A - an antibody that is secreted out of the cell layer to bind bad bacteria and renders them useless so they just pass.
  • Mucus
  • Oral tolerance
  • [Short chain fatty acids] (SCFA): Bacterial fermentation byproducts produced from [resistant starch] play an integral role in instestinal homeostasis and previnting disease. Can be used directly by mitochondria as fuel as ATP (to proliferate and do the things they need to)
  • [Resistant Starch]: the starch that is left over (not processed) by [amylase] and reach the colon
  • [Butyrate]: SCFA that is used as a fuel source for the gut [epithelium], increasing barrier integrity and limiting “leaky gut”. Induce the production of antimicrobial peptides which kill bacteria we don’t want.
  • [cytokine]: chemical messengers that float from one cell to another
  • T Cells: create Tregs and inhibit the production of th effectors
  • Regulatory T cell - called Tregs
  • [Dysbiosis]: The imbalance of bacteria in your gut. either too much of certain bacteria or too few of others
  • [Leaky gut]: As a result, bacteria and bacterial products translocate through the mucus layer into the gut tissue, causing substantial inflammation. (Your gut is letting too much of your poo into your body)
  • tolerogenic environment: an environment in your gut where you gut is in a low inflamation state where an active process of preventing an immune response occurs
  • tolerance: the active process of shutting down immune responses against non–pathogenic antigens

Energy Balance and Obesity

  • [Firmicutes] / [Bacteroidetes] ratio
  • Th1, Th2, Tregs, CD8 T cells
  • M1 and m2 [macrophages]
  • [leaky gut]
  • [LPS]: - Lipopolysaccharide- expressed by bacteria, is a powerful inflammatory factor that triggers obesity, insulin resistance, and diabetes
  • [White fat]: Stores energy
  • [Brown fat]: lots of mitochondria that are energy burning and generate heat. Takes lipid droplets ineficiently to generate heat
  • UCP1: uncoupling protein that ineficiently takes lipids and generates heat
  • [mitochondria]
  • [Akkermansia muciniphilia]: A bacteria in the gut shown to reduce many triggers for obesity… reduced insulin resistance, glucose dysregulation, steatosis, and gut permeability

Brain Connection

Modulating for health

Gut Inflamation

Notes mentioning this note

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