Understanding Digestion to Own Your Healing

A massive part of the training for nutritional therapists is centered on learning about the digestive system and digestive process in the human body. While I was doing my training and the instructors were drilling this into us and my classmates and I were sweating it out over flashcards, I didn’t realize just how important this knowledge would become for me or my practice.

I mean, I knew that if I was going to do this work I should definitely know the details, but what I didn’t understand yet was how incredibly empowering it would be for my clients when I could “demystify” it for them. Knowing how their gall bladder actually worked or what a pancreas even is or why certain points in the process mattered so much are just some of the pieces of information that have been transformative for my clients in their healing processes.

I decided that it was high time to put all that detail here on the blog, so all of our readers could take that same level of ownership with their healing. We are what we eat and understanding how that food becomes us is key. So, let’s get down to the details!

What is Digestion?

We should start by defining digestion. Simply, it’s the mechanical and chemical breakdown of food into molecules small enough to allow nutrient absorption and usability for cells.

What are the Digestive Organs?

There are 12 organs involved in some way in the digestive process:

  • Brain (bet you didn’t consider this one!)
  • Mouth (including salivary glands)
  • Esophagus
  • Stomach
  • Small Intestine (including “accessory organs” liver, gallbladder, and pancreas)
  • Large Intestine
  • Rectum
  • Anus

The functions of these organs are to ingest, secrete, mix, propel, digest, absorb, and eliminate.

So, How Does the Process Work?

Okay, here it goes . . . the process starts in the brain when you see or smell food, which triggers the production of saliva. Interestingly, the sight or smell of food also results in the brain sending a signal to halt the automatic cleansing wave action of the intestines (called the migrating motor complex or MMC) that moves food along the digestive tract at regular intervals when we are not eating.

As you can imagine, if the MMC continued while eating you’d have an “in and out” with food that was less than ideal. This is also a reason to work toward whole foods meals with sufficient supply of all the macronutrients (protein, fat, carbs) which support steady energy and require less between-meal snacking. That way the MMC is not disrupted by the brain signal at the sight and smell of food and there is opportunity for the digestive tract to be swept clean of not only food debris, but bacteria we don’t wish to take up residence.

Back to that saliva . . . The mouth is the next step in the process, as the physical beginning to the digestive tract. Here food meets mechanical and chemical breakdown. Saliva contains the digestive enzyme, amalyse, which breaks down carbohydrates. About 30% of carb digestion happens right there in the mouth between chewing and saliva, making the next phase of its breakdown, in the stomach, easier.

Once the food is all chewed up and wetted enough by saliva to swallow, it’s called a bolus. The bolus moves down the esophagus and the cardiac sphincter at the end of it opens so the bolus can move into the stomach. This valve is what keeps stomach acid away from the delicate tissue of the esophagus.

At this point, the second phase of mechanical and chemical breakdown of the bolus (food) occurs. The presence of undigested food in the stomach causes the release of a hormone, called gastrin, into the bloodstream. Gastrin triggers the muscular stomach to swish the food around, while millions of gastric glands release mucous, hydrochloric acid (HCL), and pepsinogen. The HCL and the pepsinogen start to pull proteins apart into something called peptides. Peptides are small strands of amino acids.

The purpose of the HCL is to make sure we get a very acidic environment in the stomach. The pH scale runs from 14 at the top, which is alkaline, to 0 at the bottom, which is acid. The pH needs to be around 1.5 to 3.0 (very acidic) in order to disinfect the stomach, act as our first line defense against bacteria and parasites, and break proteins into amino acid.

It also triggers the valve at the bottom of the stomach, the pyloric sphincter, to open and begin the next phase of digestion. There are many reasons that could prevent the correct acidity level being reached, but the result is that it takes longer for that bottom valve to open and the acidic contents of the stomach start to push against the valve at the top, allowing some reflux into the esophagus, which is not designed for high acid levels like the stomach. (Heartburn and GERD are often the result of stomach acid actually being too low. Read here for ways to gently correct that issue.)

The piece of digestion in the stomach is a big deal, but let’s move on to the next phase. The bolus being all churned and soak in gastric juice is now a paste called chyme. After that pyloric valve opens, the chyme moves into the first part of the small intestine, called the duodenum. The high acid and presence of the chyme is sensed and triggers the next important pieces of the process (see how important that stomach acid level is?!). First, the small intestine begins to release mucous (making things move along smoothly). It also releases two important hormones, one is called secretin and one is called cholecystokinin (CCK).

Let’s start with secretin. About 1% of the pancreas is responsible for producing the hormones insulin and glucagon, which help us regulate blood sugar, the other 99% responds to the hormone secretin by first releasing sodium bicarbonate (your body’s own baking soda!) and then releasing digestive enzymes. The sodium bicarbonate flows through a duct into the duodenum and lowers the pH of the chyme to neutral (about 7 on the scale), so it won’t burn the next delicate portions of the small intestine as it moves through the digestive tract. Reaching that neutral pH also triggers the delivery of the enzymes, to further the chemical digestive process. Amylases break down carbs, proteases break down proteins, lipases break down fats, and nucleases break down DNA and RNA.

Now, we can tackle the cholecystokinin (CCK). CCK stimulates the gall bladder to release bile through a duct into the duodenum. Bile is produced by the liver and stored and concentrated in the gall bladder. The quality of the fats we eat play a big role in the quality of the bile our liver produces (higher quality fat equals better bile). The role of bile is basically to prepare fats to be fully digested by lipase enzymes from the pancreas. Without bile we cannot properly digest fat and instead it is excreted in stool without being absorbed. This impacts our ability to take in the fat-soluble vitamins A, D, E, and K, leading to nutrient deficiencies and their accompanying health problems. (From this perspective, gall bladder removal is not actually a “no big deal” surgery.) Importantly, CCK also helps trigger the sensation of satiety.

After the full bicarbonate, enzyme, and bile treatment, chyme is totally digested and can move from the duodenum into the next portion of the small intestine, the jejunum. In the jejunum, the microvilli and villi, small finger-like projections that line the intestinal walls, plus many, many folds and pockets create a huge surface area where the job of absorbing about 90% of the nutrients that are now completely broken down in the chyme can be done. The nutrients are carried away into the capillaries, liver, and lymphatic system for use in our bodies.

The remaining chyme moves into the ileum, the last part of the small intestine, where the last bits of nutrients are absorbed. Here the chyme reaches the ileocecal valve, which is a sphincter dividing the small intestine from the large intestine. Its purpose is to prevent the bacteria and other contents of the colon from flowing backward into the small intestine, where it does not belong (malfunctions in this valve can be an underlying cause of small intestine bacterial overgrowth). This valve is also where B12 is absorbed.

The remaining chyme, which is now mostly undigested fibers, bile, water, and dead cells, moves into the large intestine. It consists of the ascending, transverse, descending, and sigmoid colon. In the large intestine the chyme is mixed with bacteria (that live in the large intestine) which convert it into vitamins K, B1, B2, B6, B12, biotin, and butyric acid (which is important to small and large intestine health). Water is also recycled by the large intestine to help condense and solidify feces and to be used in other processes in the body. This is when we reach the final part of the process. The feces is stored in the rectum and sigmoid colon until it can be eliminated from the body through the anus.

The Takeaway

The really important thing to realize when learning about the digestive organs and process is how dependent each step of the process is on the triggers occurring before it. Often the key to resolving a particular digestive issue or related health problem is about considering what signals or triggers could be off further “north.” Hopefully, this key knowledge makes it easier for you to troubleshoot and take ownership.


Nutritional Therapy Association, Inc. (2016). Module 4, Digestion and Elimination. [PDF document].

Digestive System | Everything You Need to Know, Including Pictures. (n.d.). Retrieved September 19, 2018, from https://www.innerbody.com/image/digeov.html

About Angie Alt

Angie Alt is a co-founder here at Autoimmune Wellness. She helps others take charge of their health the same way she took charge of her own after suffering with celiac disease, endometriosis, and lichen sclerosis; one nutritious step at a time. Her special focus is on mixing “data with soul” by looking at the honest heart of the autoimmune journey (which sometimes includes curse words). She is a Certified Health Coach through the Institute for Integrative Nutrition, Nutritional Therapy Consultant through The Nutritional Therapy Association and author of The Alternative Autoimmune Cookbook: Eating for All Phases of the Paleo Autoimmune Protocol and The Autoimmune Wellness Handbook. You can also find her on Instagram.


  • Linda Tyler says

    Angie, THANK YOU for taking the time to detail this incredible process! I am currently studying to be an NTC, and like you, I find that understanding the nuances of digestion has empowered me (and my new clients) to make changes that would otherwise seem abstract, to focus healing as much on digestive function as on a well-intentioned diet. Knowing how important digestion is in transforming nutrient-dense foods into the components our bodies need to thrive is foundational! Many readers will benefit by your clear, concise summary… thanks again 🙂

    • Angie Alt says

      No problem Linda! This is the nitty-gritty of what we do, right!? 😉

  • Jan Westberg says

    Thanks for such a well written article!!! I have a question regarding deciding if a particular food is negatively affecting my Ulcerative Colitis. How long after I eat something will it cause cramping and/or diarrhea? Hard for a newbie IBD to decide if it’s what I just ate that’s causing the problem or something eaten 4 or 8 hours 12 hours ago. Thanks for considering helping me with this!

    • Angie Alt says

      Generally symptoms directly related to the GI system will be experienced pretty quickly, definitely in a 12 hr window. I would start journaling carefully & see if you find a food in common w/ every instance of cramping, to help you narrow it down. Glad the article was so useful!

  • Diane says

    I think “pancreas” should be added to your list of digestive ‘organs’ even if it is technically a gland. With Sjogren’s Syndrome Exocrine Pancreatic Insufficiency (EPI) is a big problem as it causes horrible diarreah and really wretched digestive problems when food moves down into the small intestine without getting hardly any enzymes to break down fats, proteins, and starches. It brought my weight down to skin and bones. I had no idea how super important the pancreas is to digestion until this happened. I will never take it for granted again.

    • Angie Alt says

      Hi Diane! You are totally correct that the pancreas really is a crucial piece of the digestive process. If you’ll notice, it’s included on the list as part of the “accessories” that make the process in the small intestine function. I am so sorry to hear what you went through w/ Sjogren’s related EPI. I went through pancreatic insufficiency early in my celiac diagnosis & lost a lot of weight as a result too, so I truly offer some heartfelt empathy there. I hope you are doing much better.

  • Anna Givens says

    I have been on AIP for a week and trying to find digestive enzymes that are AIP compliant. Having a lot of trouble with that. I don’t know that I need HCL or of bike in them so prefer to get just the enzymes but everything seems to have unnatural or allergenic or non-AIP added stuff. Any recommendations?

    • Angie Alt says

      Anna, I can’t make supplement recommendations here. However, asking around for suggestions in online AIP support groups is likely to help you identify some great options.

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