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We all use it every day and we tend to assume it is working right as long as we don’t have major problems. We put stuff in, we get stuff out. Whatever is happening inside is happening and we don’t want to hear too much about it. Even with major issues we might be embarrassed or afraid to tell anyone what is going on. I have had to learn a lot about digestion over the past few years. It wasn’t working right for my youngest in many different ways and I had to understand what it was supposed to do and the various reasons why it might be doing something else.

By Mariana RuizLadyofHats, edited by Joaquim Alves Gaspar (i made it myself) [Public domain], via Wikimedia Commons

By Mariana RuizLadyofHats, edited by Joaquim Alves Gaspar (i made it myself) [Public domain], via Wikimedia Commons

Above is an image of the gastero intestinal system.  Now I’m going to work through it and explain what should be happening and point out some ways that that is may be not working right and why that happens.

Step 1: You eat food. It goes into your mouth and you chew it well, mixing it with saliva while you do so. This begins digestion, both the physical process of breaking it down with your teeth, and the chemical process of saliva beginning to break down starches. Did you ever do that experiment where you chew a cracker for a long time and eventually it starts to taste sweet? That is this process in action. There are two ways that this part of the process can be broken. You can not produce enough saliva. Various conditions and medications cause dry mouth. Or you could not be able to chew properly. This could be caused by a tongue tie or another problem with your mouth. In either case if the mouths job isn’t done properly digestion can be thrown off for the entire process and at the very least stress is placed upon the process further along to make up for the deficits. This is true all along the way. If a step in the process isn’t functioning correctly it will add extra stress to the following points in the process.

Step 2: You swallow your food and it travels down your esophagus into your stomach. Once in your stomach you shower your food with hydrochloric acid. This begins to break down the proteins that you have eaten. The rising acid levels in your stomach tell the opening at the top of your stomach to close and keep that acidic chyme inside and out of your esophagus. Your stomach is coated with a thick layer of mucus that protects it from this acid. The acid not only digests your proteins but it protects you from pathogens that you may have ingested with your meal. Most can’t survive the acid bath. Your stomach should be basically sterile. If you eat something without protein you don’t secrete much acid if any. If you eat something with lots of protein you secrete lots of acid (remember this is how things are supposed to work). Then your stomach starts to churn and mix the food and acid together so that it can break down the protein. The most common way that this process goes wrong is not enough acid is secreted. This is often because of low levels of the minerals (zinc is one) that the body uses to make the acid. If you don’t produce enough acid the opening at the top of the stomach doesn’t close fully. If it isn’t closed and you secrete some acid and then your stomach starts to churn that acid will splash up the esophagus. In many people this causes pain, in some it doesn’t (no one knows why some don’t feel the pain). The esophagus doesn’t have that thick layer of mucus that the stomach should have and so it can be damaged by the acid splashing up. It can rise so far that it gets into the vocal chords, the lungs, and the back of the throat and cause issues in those areas as well. For some people this is their only symptom of acid reflux, a cough, sore throat or ear pain. Another way that this process can break is if there is yeast living on the valve that closes the top of the stomach. This yeast is able to set up shop in a low acid environment and then it paralyzes this opening so that it can’t close. You could also have a problem with your mucus lining in you stomach and develop an ulcer. It was once thought that ulcers were caused by stress but then it was discovered that ulcers are caused by the h. pylori bacteria. Remember your stomach should generally be sterile so it was low levels of stomach acid that let this situation start in the first place.

Step 3: After a while the opening at the bottom of your stomach opens up and the chyme moves into the doudenum. At this point the chyme is white. There the pancreas showers the food with a base (like baking soda) to neutralize the acid coming from the stomach. It also is the point when bile is added from the gall bladder in response to fats in the food (this turns the food dark) and also enzymes from the pancreas are released to further break down the food so that the body can absorb it and benefit from it. Your small intestine is lined with finger like projections called villi that secrete enzymes to break down food and mucous that protects the gut wall from damage. This is also where the nutrients are absorbed from your food and travel into the blood stream. Another important thing that this food does is feeds the billions of “others” in your digestive tract. These are beneficial bacteria, yeasts and even viruses that live there and have developed a symbiotic relationship with us. They help break down our food and generate vitamins to nourish us as a byproduct. They also keep in check those pathogens that make it past the acid in the stomach. The food travels through the small intestine where it is broken down and most of the nutrients are absorbed. This process can malfunction in a few ways. First if you have gall stones or no gall bladder at all you may not secrete enough bile because of this to break down the fats you take in. This means that those fats (and the fat soluble vitamins they contain) will pass through your body undigested and unabsorbed. This can lead to nutritional deficiencies. Also the lining of your digestive tract can be damaged and missing your mucous barrier. This means that you won’t be secreting the enzymes necessary to digest the food and it will either pass out of your body unabsorbed or it will pass through the gut wall and into your blood stream unbroken down. As you can imagine, this is not a good thing. This is referred to as a leaky gut and can be very difficult to recover from. Another way that this can be broken is if you don’t secrete enough acid in your stomach the pancreas won’t get the signal to release enough enzymes to break down the foods it is responsible for and so those foods will pass through you undigested as well.  And then there are the multitudes of others that should be helping you out, digesting foods, destroying pathogens and generating vitamins for your body to absorb. If they are not nourished by what you eat or if they aren’t in sufficient quantities to do the good that your body counts on for health, then you will be lacking the important vitamins and minerals you need.  Also, you won’t be fighting the over-growths of pathogens that you don’t need.

Step 4: What is left of your food moves into the large intestine where the water it was mixed with is absorbed back into the body and some more bacteria work on it. Then it is eliminated from the body 1-3x a day. What comes out should be soft but formed, like a thin log and dark (see number 4 on the bristol stool chart).  It should hold together in the toilet. It shouldn’t have any discernible pieces of food in it and should be uniform in color. There is much debate about if it should sink or float and interesting arguments on both sides. Stool is bulked by dead bacteria and also indigestible fiber. Again there is debate about how much fiber is healthy. I’ll just say that fiber is not necessary for a healthy bowel movement to happen. In fact food isn’t necessary since stool is also bulked by dying bacterial cells. If the stool is bulked primarily by fiber it will float while if it is bulked primarily by dead bacteria it will sink. This process can break is a few ways. If there isn’t enough bacteria in the large intestine or the wrong kind you can have gas or bloating. If you don’t listen to the urge to defecate you can stretch out your colon and end up constipated and needing to pass very large stools. Or you might have the opposite problem and too much watery stool. This can be caused by irritation in your gut. Your body sees this as a problem/possible pathogen and is trying to purge it before things get worse. Right at your anus you have hemorrhoids. These are there to lubricate the stool and make it easy to pass. If you pass very large stools and have to strain to pass them you can do damage to this structure and cause it to swell and bleed or even extend outside your anus.

Here are couple more issues that can impair digestion:

A condition called eosynophylic esophogitis can cause problems with eating. This is somewhat like an allergic reaction that happens locally in the esophagus. This can result in choking on foods and also reflux like pain and vomiting. This is a reaction that is triggered by proteins, usually from foods but can also be triggered by environmental substances, like pollen, that are inhaled and cause this reaction. The basic treatment for this is to identify and avoid the triggering substances. There is much more to this but I need to restrict the scope of this post somehow.

About stomach acid:  you may have been told that your reflux is caused by excess stomach acid and that the only cure is to take a medication that reduces that stomach acid. Unless your Dr did a test on your stomach acid levels there is no way to know for sure what caused it.  However no matter what the cause, reducing your stomach acid down to zero will stop the pain. It will also greatly impair your ability to digest your food and it will turn off one of the main ways your body protects you from pathogens. Pharmaceutical  companies haven’t figured out how to increase your stomach acid to the right levels in a simple once a day for the rest of your life pill but they have figured out how to stop your stomach acid that way. It is a very lucrative business and they are happy to educate your Dr for free as to why their pill is the best one to do the job. Once you start taking those sorts of drugs you are usually going to be a customer for life.

Also, there are gall stones that I mentioned up above.  Your body puts some toxins it is trying to get rid of into the bile. The cholesterol in the bile emulsifies this mixture and keeps it mixed up well so that it is eliminated as a liquid. If you don’t have everything emusified, then some solids can precipitate out and form gall stones. These gall stones can then block the ducts and cause pain and make it hard to digest fats since they block the release of bile. Also if you don’t eat much fat you won’t be releasing the bile regularly and in big enough quantities to fully clean out the gall bladder. This can also lead the the creation of gall stones. A low fat diet can prevent the pain of the gall stones passing through the bile ducts but it doesn’t exactly fix the problem.

Hopefully this has educated you more about the digestive process and how it should be working.  If you have any questions or anything to add I would love to hear it in the comments section.


  1. How informative! Makes so much sense the way you presented it. Thanks a ton!

  2. Becky Jacobs

    Nice summary of the gastrointestinal system from one end of the tube to the other!! 😉

  3. Barbara Lehr

    Fantastic post! Fearfully and wonderfully made indeed!

  4. This is great, I will use it to teach my kids about digestion in the coming homeschool year… the only other thing I wish it had is mention of how refined sugar impairs/damages these processes… having a hard to convincing my 10 and 11 year old kids 😉

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