Digestion: From Top to Bottom

All disease begins in the gut – Hippocrates


So often overlooked or taken for granted… but just about everything in nutrition and health revolves around this simple yet amazingly complicated process. My goal with this post is to overview the digestive process and share some valuable information on the basics, a few tips and some potential things to pay attention to. Although this review will merely scratch the surface of the intricacy of digestion, hopefully at the end you will have broken it all down, absorbed what you needed and passed on what you didn’t (pun intended – of course!).

So let’s dive right in take a journey through the digestive process…

Digestion 101

Digestion is both literally and figuratively a top down process, or “top to bottom” journey. Digestion starts in your head and finishes down below, with a number of intricate and complex processes between the start and finish.

What is “digestion”?

The simple answer… the process by which the digestive tract accomplishes three things: the breakdown of food into usable parts for absorption into cells in the body, protection from invading organisms and toxins, and disposal of waste products.

The first aspect of digestion is about mechanical and chemical food disassembly. Breaking food down, in stages, into fatty acids, amino acids, simple sugars and nutrients which the body can absorb and use for normal functioning. The second aspect is concerned with protecting us from pathogens and foreign bacteria that enter the digestive tract. The acidity of the stomach is key in killing microorganisms and the largest part of the body’s immune system is in the lining of the intestines. The digestive system has it’s own nervous system that is often termed the “second brain.” Lastly, digestion ultimately results in removing waste from the body.

What is the digestive tract?

The digestive tract, from top to bottom, is approximately 30 feet long, has a surface area of a tennis court and typically processes food in 24-72 hours. In essence, the digestive tract is a tube that runs from your mouth to anus, separating “not in your body” from “in your body” much like the skin. Each stage of the tract, separated by muscles and valves, breaks down food mechanically and chemically. The body absorbs valuable material and moves along non usable or offensive material. Each stage of the process has a unique and important function and relies upon the processes before and after it for optimal digestion.

Here is a simple look at the digestive tract and the key places we will visit in our journey through the digestive process…

From Top…


Mouth & salivary glands



Pancreas, Liver, Gall Bladder

Small intestine

Large intestine


To Bottom…

What happens during digestion?

Here’s the quick outline of the digestive process…
You think about, see or smell food.
The body releases saliva and prepares digestive juices.
The mouth chews food to break it into a mushy paste.
Salivary enzymes act to soften the food and start breakdown of carbohydrates and fats.
Swallowing transports the food down the esophagus and through the esophageal sphincter into the stomach.
The stomach churns and mixes the food with acid and gastric juices to further break down the paste, initiate protein degradation and kill undesirable microorganisms and pathogens.
Once mixed well the food paste is considered chyme and the pyloric valve allows passage into the small intestine.
The gall bladder releases bile to start breaking down fat.
The pancreas releases enzymes to further breakdown carbohydrate, protein and fat.
The small intestine begins to absorb the completely broken down nutrients (fatty acids, amino acids, simple sugars, vitamins and minerals) through a permeable skin of micro villi on the walls of the intestine.
The nutrients undergo an immune system screen and then travel to the liver.
The liver screens, filters and processes the nutrients before sending them out into the bloodstream to feed the cells in the body.
Muscles continue to move the chyme along the small intestine, while the breakdown of food continues and the body continues to absorb, screen and filter the particles.
Whatever does not get absorbed moves through to the large intestine (colon).
Bacteria residing in the colon feed off the food remains, creating nutrients we absorb (vitamins, fatty acids) and other byproducts, some of which we use, some we don’t.
The colon extracts water from the liquid waste as it moves along, recycling it into the bloodstream.
Once moved through the colon, the food has become fecal matter, consisting of mostly excess water, dead bacteria, indigestible fiber and some other materials not needed by the body.
The fecal matter moves to the rectum for storage.
When signaled, the body moves it out the anus, eliminating the waste from the body.

And that, folks, is digestion.

For more detail, let’s take a deeper look at each phase/stage…


Digestion starts with your brain. Most specifically, your nervous system. There are two main branches: sympathetic and parasympathetic. Sympathetic is “fight or flight” and parasympathetic is “rest and digest”. Simply put, eating in a relaxed state enables everything to operate in the ideal state, maximizing digestive potential. Eating under stress, on the go or in a hurry will compromise the body’s ability to digest properly. Stress hormones/processes inhibit digestion by shifting the body’s focus and resources away from the intestinal tract, which can create several problems throughout the digestive chain. The onset of digestion typically begins with thoughts, sights or smells of food. Upon one of these stimuli, the brain signals the body to prepare for food. The digestive glands/organs start preparing their respective enzymes and juices to anticipate the introduction of food into the body. The longer the body has to prepare the better. This is one of the reasons why cooking and/or preparing your own meals gives the body the most ideal digestion platform and feedback. If the body is well prepared it will “tell” you how hungry it really is and give you more accurate signals when it it is full. The psychological thoughts, actions and aromas that take place during food preparation, when paired with a relaxed state, set the ideal foundation for proper digestion.

Mouth & Salivary Glands
This is where most of the “physical” breakdown of food takes place. The primary function of the mouth is to turn large chunks of food into a mushy paste. The salivary gland releases saliva, containing amylase, to start breaking down starch. Also included in saliva are enzymes to start cleaving fat and mucus to soften the food. The longer you chew, the more time your body has to fully prepare the food for the stomach and the more surface area there will be for enzymes to effectively act on. Swallowing larger chunks of food can moderately (or even severely) impair the digestion process, making the stomach work harder to break down the food. Additionally, saliva has anti microbial properties so chewing longer and more thoroughly allows it to effectively kill bacteria.

The 10-12 inch tube that channels the food into the stomach via the esophageal sphincter. The esophagus is lined with muscles that push the food down through peristaltic (wave like) contractions. The better food is chewed, the more easily it will get transported to the stomach. Swallowing partially chewed food or swallowing too quickly can lead to choking or air entering the esophagus with the food (hiccups are a common result).

Stomach & Pancreas
The stomach serves two primary purposes. First, it is a storage tank, about 25 cm long with 4 liters volume (this varies from person to person and depends on the typical size of your meals). Second, the stomach is a churning and mixing organ. It continues mechanical breakdown while chemical breakdown really begins to concentrate. The stomach lining contains gastric pits and mucosa which release gastric juices (HCl – hydrochloric acid) and pair with enzymes from the pancreas to initiate protein breakdown and further digest carbohydrates. The environment of the stomach is key for the digestive enzymes to work properly. It needs to be very hot (temperature) and acidic (ideal pH is around 2-3) to effectively allow the enzymes to dissolve food and transform it to the semi-liquid form known as chyme, which is what gets passed into the small intestine. When the pyloric valve senses chyme with the correct acidity/ph, it allows passage into the small intestine. Many problems in the realm of heartburn and reflux actually stem from stomach acid being not acidic enough to effectively break down food and pass it to the next stage or getting passed back into the stomach ineffectively. Drinking cold beverages or too much liquid with or immediately before meals can inhibit the digestive process by cooling off and diluting stomach acid and stress (both acute and chronic) hinders the body’s ability to produce and maintain the proper acidity.

Liver & Gall Bladder
At the entrance to the small intestine (SI) lies the gall bladder. When chyme enters the SI, the gall bladder is stimulated to release bile, made in the liver, to breakdown fats into smaller fatty acids. Bile also acts to neutralize the acidity of the chyme from the stomach, which allows for better nutrient absorption in the small intestine. Good functioning gall bladder response is important to maximize digestion. Among other things, a perpetual low-fat diet or high polyunsaturated fat consumption (vegetable/seed oil) can lead to static gall bladder/bile action. This system is like all others in the body, following a “use it or lose it” protocol. Regularly stimulating the gall bladder to release bile (and the liver to produce bile to replenish storage bile) will keep the system running smoothly and limit build up in the gall bladder (i.e. stones).
The liver has many functions overall but during digestion it is responsible for bile production, filtering, toxin removal and nutrient processing. Nearly everything that you eat goes through your liver, so think of it as the “customs” process for entry into the United States of Your Body. It will deal with each substance in the necessary way, and things that bypass the liver usually cause trouble. However, just because the liver processes it does not mean it is not harmful and will be productive. It is merely a filter and can often allow toxic substances through, particularly if it gets overwhelmed. How does it get overwhelmed? Stress, toxins and bad food. The biggest offenders: refined foods/drinks containing excess sugar/fructose/alcohol/polyunsaturated/trans fats/chemicals/preservatives, not to mention drugs of all kinds- particularly ones used for medication. Long story short, if your liver gets overwhelmed, your ability to filter and screen substances diminished and the rest of the body will suffer.

Small intestine
The primary function of the small intestine is nutrient absorption. Everything you get from your food happens here. The SI is about 20 feet long and functions much like a conveyor belt. Muscles contract to move the contents along in a process/action called peristalsis, which resembles a wave like motion. The pancreas and liver contribute enzymes and digestive juices which, along with juices from the SI, keep degrading fats, proteins and carbohydrates into the most usable, simple forms. The walls of the SI are covered with billions of finger like projections called villi (which have smaller microvilli) that create a permeable skin with an immense surface area, where the actual absorption of nutrients into the body occurs. The villi of the intestine are covered in cells that are separated by junctions that control the access into the body. If these junctions are not working properly, unwanted molecules can gain access to the body (bacteria, pathogens or larger food particles) leading to an immune response. Most food allergies are created through this malfunctioning of the intestinal lining, which can also lead to a host of other problems.
As nutrients absorb throughout the SI, the body channels them through a complex lymph system. If a foreign/unrecognized particle enters, the immune system reacts immediately, attacking and/or creating antibodies to that particle. Once the body identifies an invader, it can cause a reaction each subsequent time the body senses and recognizes it. This sensitivity can also cause immune based reactions to similar particles (usually proteins), which is why food allergies/reactions don’t always arise from just the original offending food. Once the gut lining is compromised the immune system will be on high alert for foreign particles. If the junctions between the cells are damaged, more and more particles can enter the permeable skin and more immune reaction will ensue. The result is a cascading cycle of inflammation and irritation. If you have systemic inflammation (arthritis, autoimmune, eczema, bowel discomfort, acne, etc.), chances are there is some disruption of the integrity in your small intestine. What disrupts the SI? Grains (wheat and gluten in particular), dairy, legumes, and other foods with high concentrations of lectins are the biggest problem for most people, although sugar and some types of vegetables can also be very damaging to the gut lining, particularly when it is already inflamed and vulnerable. Once again, both acute and chronic stress tremendously affect your body’s ability to manage the gut lining and immune reaction to foreign particles.

Large intestine
After the chyme works through the SI, it enters the large intestine (colon or LI) for the final stages of digestion. Approximately 5 feet long, the large intestine is primarily responsible for bacterial homeostasis and water retention. The colon typically processes chyme in 12-16 hours in a healthy state. Although no more food breakdown occurs, the LI houses one of the most important environments in the body. Most of the bacteria in your body reside in the colon. Although often considered problematic, bacteria are critical to our health and immune system. Actually outnumbering our own body cells 10 to 1, bacteria provide a number of necessary functions to humans and are key to optimal health and digestion. We live in a symbiotic relationship with bacteria. They help provide us with several things and we provide a nice environment for them to live. As the bacteria feeds on particles and food passing through the colon (primarily fiber), they create vitamins such as vitamins B12, K, riboflavin and thiamine, along with turning indigestible fiber into short chain fatty acids. It is the bacteria in the intestines that help regulate immune function and keep other “unwanted” or foreign bacteria from taking up residency. When you hear “probiotics” touted for health, it is for this reason. These are the bacteria that help keep us healthy. Related to them are prebiotics which, in essence, are fiber that helps feed the good bacteria in the colon. Regulating the bacterial environment in your gut lies at the heart of disease and immune function. How can you optimize bacteria in your gut? The easiest way is to incorporate foods with live bacteria into your diet and then feed them with fiber. Think cultured and fermented foods, such as yogurt and kefir, sauerkraut and kimchi, natto and tempeh, kombucha, some cheeses and any other cultured or fermented food you might come across.
The second function of the colon is to extract water from the chyme for recycling into the body and compact the fecal matter to store in the rectum for elimination. It is quite common (but not normal or natural) to have a problem with constipation or irregularity and this is often a result of dehydration. If the body is in need of water, it will hold fecal matter in the colon longer to extract out as much moisture as possible. The longer it stays in the colon and the more dry it gets, the harder it is to move along. Fiber supplements will aid in the speed through the digestive tract but may just push the food/waste along independent of the problem. Drinking more water or eating more water based foods with fiber (fruits and vegetables- I know, shocking) should be the first course of action to help restore regular bowel function.

The elimination of food, when everything has run its course, should be pretty simple. The rectum is the last stop along the digstive process and serves as a holding tank for fecal matter to accumulate for elimination. When then body has built up enough matter or gets stimulation to eliminate (which can be from a number of things- ingesting fat for one), the process is straightforward. Waste should be easily discharged, semi-soft, brown colored, and an S or C shape (check out the Bristol Stool Scale for a guide to elimination). Elimination should provide a sense of relief and full emptying. If any of these are not taking place, it is a sign of something wrong. As my young son once elequently stated, “I like to poop. It feels so good.”

And that is Digestion 101. Let’s hope digested it all, absorbed what you needed and eliminated the waste.

I plan to expand more in the future and put together a “digestion dos and donts” post with some more tips and troubleshooting ideas that can address more specific intestinal issues. Digestion is vitally important part of our health yet so many people struggle with minor (and often major) problems associated with the process. Most of those can be managed or even eliminated with interventions ranging from small tactical adjustments to a complete digestive overhaul. Hopefully the end result is much better digestion and a higher quality of life. But that’s another post for a later date.

In the meantime, let’s wrap it up.

The Bare 5 Bottom Line on Digestion:

1. Don’t take digestion for granted. Problems with digestion is not normal. Without a healthy digestive tract and system, body health is impossible.
2. Eat in a relaxed state. Stress is horrible for digestion.
3. Chew your food well when you eat. Relax and let your body digest after eating.
4. Include cultured and fermented foods in your diet.
5. Drink more water between meals, less during meals.

Thanks for reading, have a great Thanksgiving week! It will provide excellent practice for the tips above!



Please log in using one of these methods to post your comment:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s