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Digestion: Top to Bottom

When we mention “gut health”, we are referring to more than just your stomach and intestines. A well-functioning gut is devoid of inflammation, infection, and imbalances such as dysbiosis or bacterial overgrowth. It hosts a rich and diverse community of gut bacteria, facilitating effective digestion and absorption of nutrients from food.

In this article, we will examine the process of optimal digestion from start to finish.

Figure 1: Sites of Digestion 
image depicting where nutrients are digested


As we bite into food, the process of digestion kicks off with chewing. This mechanical action breaks down the food into smaller, more manageable pieces. Meanwhile, saliva, secreted by the salivary glands, moistens the food and contains enzymes like amylase, which starts breaking down carbohydrates into simpler sugars. In today’s busy world, most of us do not take the proper time to chew our food thoroughly. However, this simple act is important to starting an optimal digestive process. 

A lack of saliva, or dry mouth, can increase the risk of dental decay, gum disease, and oral infections due to reduced protection against bacteria. Dry mouth can also impair swallowing and cause a decreased sense of taste. Chronic dry mouth may be indicative of underlying health issues such as autoimmune diseases, hormonal imbalances, or medication side effects. 


Once adequately chewed and mixed with saliva, the food bolus is swallowed, traveling down the esophagus via peristalsis, a series of muscular contractions that push it towards the stomach.

The esophagus, while seemingly simple in structure, can be prone to a variety of conditions that affect its function and health. The lower esophageal sphincter (LES) is a ring of muscle that sits at the bottom of the esophagus. It separates the esophagus from the stomach and aims to protect the esophagus from acid in the stomach. When the LES is too relaxed, it can lead to problems such as reflux and esophagitis. 

Gastroesophageal reflux disease (GERD) is a common issue where stomach acid flows back into the esophagus, causing heartburn and sometimes chest pain. Esophagitis, which involves inflammation of the esophageal lining, is often caused by GERD, infections, or certain medications. Lastly, esophageal strictures, or narrowing of the esophagus, can occur as a result of chronic inflammation or scarring, causing difficulty swallowing. 


When food reaches the stomach, it encounters a harsh acidic environment, thanks to the secretion of hydrochloric acid. This stomach acid, along with enzymes like pepsin, starts breaking down proteins into smaller pieces. 

Stomach acid also aids in the absorption of essential nutrients. One such nutrient is vitamin B12, which requires stomach acid for its release from food and subsequent absorption in the small intestine. Without adequate stomach acid, the absorption of vitamin B12 and other nutrients may be impaired, leading to deficiencies and related health issues. If stomach acid levels are excessively high, it can result in conditions like GERD, ulcers, and Barrett's esophagus, which can cause discomfort and pain. Conversely, low stomach acid levels can lead to symptoms such as indigestion, bloating, and nutrient deficiencies.

Small Intestine

The next phase of digestion occurs in the small intestine, where the majority of nutrient absorption takes place. Here, digested food is further mixed with bile from the liver and enzymes from the pancreas. Bile breaks fat into smaller droplets, while pancreatic enzymes continue the breakdown of carbohydrates, proteins, and fats.

The lining of the small intestine is covered in tiny finger-like projections called villi. Nutrients like vitamins and minerals are absorbed through these structures and transported into the bloodstream to be used by the body. Celiac disease, an autoimmune condition, disrupts the function of these villi, leading to numerous symptoms that can extend beyond the digestive system. However, a more common condition seen in the small intestine is small intestinal bacterial overgrowth (SIBO). SIBO occurs when too many gut bacteria end up in the small intestine instead of the colon. While SIBO is significantly underdiagnosed, one study found that up to 78 percent of patients with irritable bowel syndrome (IBS)  also tested positive for SIBO (1). This suggests that SIBO may be a root cause of IBS.

Large Intestine (Colon) and Rectum

As the digested food moves through the last parts of the small intestine, any remaining water and electrolytes are absorbed, forming stool. These waste products then pass into the colon for further dehydration and compaction. 

The colon also houses a vast community of beneficial bacteria known as the gut microbiota, which play crucial roles in nutrient absorption, immune function, and overall well-being. 

Finally, the stool is stored in the rectum until it is ready to be eliminated from the body through the anus.

Dysbiosis, or an imbalance of gut bacteria, is the most common disorder affecting the colon. When dysbiosis occurs, it can lead to digestive issues like bloating, gas, and diarrhea, as well as immune system dysfunction, inflammation, and an increased risk of developing autoimmune diseases. Restoring balance to the gut microbiota through dietary changes, probiotics, and lifestyle modifications is key to addressing dysbiosis and promoting optimal health. Learn more about our favorite soil-based probiotics to reduce dysbiosis.

Key Takeaways

Digestion is a complex process that involves coordinated efforts of various organs and enzymes. From the initial act of chewing in the mouth to the absorption of nutrients in the small intestine and the elimination of waste in the colon and rectum, each step plays a vital role in our overall health. 

Many chronic symptoms stem from gut-related issues. Learn more about our functional medicine program to optimize your health and treat your symptoms from the root cause. 

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