The Stages of Digestion & How Enzymes Help

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You probably don’t give much thought to digestion, since it’s an involuntary activity that happens whether you think about it or not. Sure, you decide what, when, and how much to eat—though even this sometimes seems to be beyond our conscious control. 

But before your body can use the food you eat every bite must be broken down into simpler nutrients. This requires a complex collaboration between your brain, nervous and endocrine systems, gastrointestinal tract, and accessory organs such as the pancreas, gallbladder, and liver. Even the bacteria in your gut play a part! 

As a naturopathic doctor, I recognize the importance of optimizing digestive function for overall health and well-being. I also believe in the power of knowledge—that an understanding of basic physiological processes leads to better lifestyle choices, compliance with supportive therapies, and health outcomes. 

To that end, let’s review the digestive process, its stages—including the critical role of digestive enzymes—and how the food you eat is transformed into nutrients that keep you alive.

Digestion Begins in the Brain

The first stage of digestion is the cephalic phase, derived from the Greek word for “head.” Although this stage is also referred to as ingestion, it actually begins even before you take your first bite. The mere smell, sight, or even thought of food stimulates your salivary glands and primes your body for digestion. 

Two other stages of digestion also start in the mouth and continue throughout the gastrointestinal tract:

  • Mechanical digestion: Chewing is a mechanical or physical activity that grinds and mashes food into smaller pieces that can be swallowed. Saliva makes chewing and swallowing easier. For optimal digestion, I recommend chewing each bite at least 20 times.
  • Chemical digestion: Digestive enzymes break food into simpler compounds and ultimately into small molecules that can be absorbed into the bloodstream. Amylase is an enzyme produced in the salivary glands that kick-starts the chemical digestion of complex carbohydrates like starches. This is why I often recommend taking a good digestive enzyme supplement that includes amylases to help facilitate digestion.

Swallowing & Movement Through the Esophagus

When you swallow food, it leaves your mouth, goes into your pharynx, and is propelled down your esophagus into your stomach. 

This propelling movement—which is called peristalsis and also occurs in the stomach and small and large intestines—consists of wave-like contractions of the smooth muscles in the walls of the esophagus. Propulsion is an appropriate term because peristalsis is so forceful that you could even swallow if you were standing on your head (not that I’d recommend it).  

A sphincter, or ring of muscles, at the bottom of the esophagus relaxes and opens to allow food to pass into the stomach and closes to keep stomach contents out. Heartburn, indigestion, and other symptoms of gastroesophageal reflux disease (GERD) are caused by stomach acid backing up into the esophagus.

Mechanical & Chemical Digestion in the Stomach 

Mechanical and chemical digestion in the human digestive system shifts into higher gear in the stomach. Cells in the lining of the stomach secrete strong gastric acids (primarily hydrochloric acid), which along with the churning activity of peristalsis turn food into a soupy mixture called chyme. 

Stomach acids also activate pepsin, a digestive enzyme that starts breaking protein into smaller peptides and amino acids. Fat digestion begins as well with the release of gastric lipase, an enzyme that tackles fats.  

Enzymes, Bile & the Small Intestine

Chyme then moves into the small intestine, where most digestion takes place. It triggers the release of hormones that signal the liver, gallbladder, and pancreas to produce enzymes and other substances that are essential for the digestive process. They include: 

  • Bile: Produced in the liver and stored in the gallbladder, bile is released into the duodenum, the first section of the small intestine. Just as detergent makes it easier to remove oil and grease, bile breaks fat globules into tiny droplets and reduces their surface tension so they can be more easily digested. 
  • Lipase: This digestive enzyme, secreted by the pancreas as well as the stomach, takes over where bile leaves off. Pancreatic lipase further splits fats into simple lipids like fatty acids and glycerol that can be absorbed.
  • Protease: The pancreas also produces enzymes that degrade proteins into small peptides and amino acids. Called proteases or proteolytic enzymes, they include trypsin and chymotrypsin. 
  • Amylase: Also found in the saliva, amylase is an enzyme that converts starches and other long-chain carbohydrates into shorter, simpler sugars like glucose. Pancreatic amylase is responsible for the bulk of carbohydrate digestion.

If you have trouble digesting certain foods, your pancreas may not be producing enough of these enzymes. Supplemental enzymes, taken at the start of meals, have helped many of my patients overcome common digestive complaints.

Absorption in the Small Intestine 

The entire process so far has been to break food into smaller and simpler components, with enzymes involved in each step along the way towards the ultimate goal of digestion, which is absorption.

The small intestine, which averages about 20 feet in length, is lined with tiny finger-like projections called villi and microvilli. This is where glucose, amino acids, vitamins, minerals, and other nutrients are absorbed into the bloodstream. Fatty acids take a more indirect route, transported from the intestine to the blood via the lymphatic system. 

These life-sustaining substances are then delivered to cells and tissues throughout your body.

Large Intestine & Gut Microbiota 

From there, undigested food, fluids, and waste materials move into the large intestine, where the final stages of digestion take place.

Some of the undigested food is broken down by the gut microbiota—the trillions of bacteria and other microbes that reside in the intestine. During this process, important metabolites such as vitamin K, B vitamins, butyrate, and other short-chain fatty acids are produced. The gut microbiota also supports nutrient absorption and elimination—not to mention immune function, blood sugar, and even mood, appetite, and weight. That’s why I often recommend probiotics and prebiotics. They support a robust, diverse gut microbiota, which is essential for optimal health

During this transit, water is absorbed, stool gains its usual consistency, and waste is eliminated from the body via bowel movements.

In Summary

Problems occur when any of these stages of digestion is out of whack, so it’s no surprise that digestive complaints are so common. 

The good news is that there are proven natural therapies that enhance every stage of digestion—from eating a healthier diet and chewing your food thoroughly to treating GERD and constipation with herbal remedies to taking digestive enzymes and probiotics for overall digestive health.

Dr. Drew Sinatra

Meet Dr. Drew Sinatra

Dr. Drew Sinatra is a board-certified naturopathic doctor and self-described “health detective” with a passion for promoting natural healing, wellness, and improving quality of life by addressing the root cause of illness in patients of all ages. His vibrant practice focuses on treating the whole person (mind, body, and spirit) and finding missed connections between symptoms and health issues that are often overlooked by conventional medicine.

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