Anatomy and Physiology of the Gastrointestinal Tract

We get to talking a lot on this blog about the gut, the gastrointestinal tract, the microbiome, the small intestine, the stomach, the large intestine, poop. You know, we really run the gambit. But, without a basic understanding of what the heck the gastrointestinal system is and how it works, there could be a little confusion when we discuss certain bacteria and pieces of anatomy.  

Knowing how something works is half the battle to fixing it. So, we are here to help you figure out exactly what happens to your food after you swallow.  

There are two main groups of anatomy when discussing the digestive system, the gastrointestinal tract and accessory digestive organs. As you dive deeper into the world of the gut, you will find that the accessory digestive organs are just not given their fair share of airtime. But, they are in fact extremely important in the digestion of your food, which is kind of what the gut is all about. But, as unfair as it is, we spend most of our time on this blog talking about the intestines, and for the most part when we use the word, “gut“, we mean the large intestine.  

Now that we have that disclaimer out of the way, let’s discuss your innards.  

Oral Cavity

I mean, this seems like the natural place to start, right? Where do you put your food when you eat? So, let’s start this journey in the mouth.  

The oral cavity is your home for your teeth, tongue, and salivary glands. All three are accessory organs meant to aid in digestion but do not do the actual digesting. This is the first step in the digestion process, ingestion.  

Your teeth are little organs with their own nerve system and blood supply, they are the hardest organs in your body meant to chew food into smaller pieces (but, you already knew that!)  

While the food is being chewed, it is being moistened by saliva, the salivary glands main job is to keep everything from the mouth to stomach wet, allowing food to easily transition from one location to another. Saliva contains amylase which begins the breakdown of carbohydrates.  I do not want to get hung up on all the specifics, but there are quite a few salivary glands throughout the oral cavity meant to keep everything lubricated and begin the digestion of your dinner.  

Last but certainly not least, the tongue. The tongue is basically a muscle with taste buds on it. The taste buds allow you to, you know… taste your food. Then the muscle that is your tongue allows for food to be moved around within the mouth, soaking it in saliva, then it shoves food to the back of your mouth moving it into position for swallowing. 

Throat and Esophagus

At the back of your mouth is the opening to a tube called the pharynx. “Pharynx” is just a fancy word for throat tube, it is the tube that leads from the back of the mouth to the esophagus. The pharynx contains a flap (the epiglottis) which either allows food to go to the esophagus or air to go to the larynx, so you can breathe.  

The esophagus is a long tube attached to your Pharynx. This tube carries swallowed food along its length and deposits it into the stomach, the lower end of the esophagus is a sphincter called the esophageal sphincter that locks food in the stomach, another part of the ingestion process. 


Your stomach is a muscular pouch that is roughly the size of your two fists side by side. This is where food sits that is waiting to be digested. It is filled with digestive enzymes as well as hydrochloric acid that both help continue the process of digestion while the food is on its way through. The stomach allows you to eat just a few times a day, it holds more food than can be processed at one time by the small intestine. This is the final piece of the ingestion stage of digestion.  

Small Intestine

The small intestine is a tube about 1 inch by 10 inches in length, small and thin, allowing it to coil up within the abdominal cavity. The small intestine is attached to the stomach and is the next stop for your dinner on the way through the GI tract.  

Because of the long and thin nature of the small intestine, the tube has many switchbacks in it, allowing for maximum time for proper absorption of nutrients. Because of the acid in the stomach and the small intestines close proximity to its acidic friend, very few bacteria call the small intestine home. The magic of the microbiome mostly happens in the large intestine

Liver, Gallbladder, and Pancreas  

These extremely important accessory organs are necessary for the digestive enzymes and bile for breaking down your meals. The liver is the second largest organ in the body weighing in at about 3lbs is best at creating the bile needed in the small intestine for digestion. The liver can be found just to the right of your stomach.  

The gallbladder actually stores excess bile for later use but does not create it. The gallbladder can be found snuggling with the liver, sitting just behind it, next to the stomach.  

Finally, similar to the liver, the pancreas is responsible for creating digestive enzymes for use in the small intestine during digestion. Your pancreas can be found just under the stomach sandwiched between the sac holding your lunch and your small intestine.

Large Intestine  

Again, a tube, just larger than the small intestine. The large intestine also known as the colon is where the small intestine dumps all of its unused waste, it is about 2.5 inches wide and 5 inches long.  

When it comes to the microbiome, this is where most of the action happens – wonder no more. (When it comes to the what? – Don’t worry, we have you covered. An intro to the microbiome.)  When we are discussing gut bacteria and microbes, this is where the magic happens. The colon is the perfect home for bacteria (also, yeast and fungus), because of its dark, wet, filled with bacteria food nature. The large intestine is where all the waste that could not or was not previously absorbed ends up. This includes fibers left undigested which turn into feces which is expelled out the anal canal through defecation.

Stages of Digestion  

Here are the 6 processes that the digestive tract utilizes to turn your food to feces: 

    • Ingestion (mouth, throat, and stomach) 
    • Propulsion (movement of food from the stomach along the course of the GI tract)
    • Mechanical breakdown (chewing done in the mouth)
    • Chemical breakdown (digestion – done primarily in the small intestine)
    • Absorption of nutrients (done through the walls of the intestines)
    • Defecation (elimination of waste done at the tail end of the colon and anal canal) 

We know that when doing research on the GI tract, it can become overwhelming pretty quickly. There really is a lot going on in there.

I hope that we were able to simplify the process for you and that you were able to get a very broad overview of what is actually happening after you put those tacos in your mouth.

If you would like a more in-depth explanation of the digestive tract, accessory organs, and how exactly your food becomes poop, head over here.  

If you are curious about gut health and how it can (negatively) affect your body, head over here. 
Last but certainly not least, if you want to know what the heck is up with prebiotics and probiotics. you can find articles on that exact topic:
What are Prebiotics? 7 Reasons You Need Them Today (& Best Sources!)
Why Your Body Needs Probiotics Today: No, Yogurt Won’t Cut it

If you want to schedule a one on one consultation, I would be honored to help you reach your goals. Just follow this link.

I think that is about all!


love your guts, love others, and do good.