Understanding Digestion: What Happens to Undigested Carbohydrates?

October 19, 2025 •

3 min read

Approximately 5-20% of dietary starch resists digestion in the small intestine. So, what happens to undigested carbohydrates? The answer is a fascinating journey involving billions of bacteria in your large intestine, which turns this indigestible matter into beneficial compounds crucial for your health.

Quick Summary

Undigested carbohydrates, primarily fiber and resistant starch, travel to the large intestine where they are fermented by gut bacteria. This process produces beneficial short-chain fatty acids (SCFAs), but in cases of malabsorption, it can cause digestive distress like bloating and diarrhea.

Key Points

Normal Process: Undigested carbohydrates like fiber and resistant starch are fermented by bacteria in the large intestine.
Short-Chain Fatty Acids (SCFAs): The fermentation process produces SCFAs (butyrate, propionate, and acetate) that provide energy and health benefits to the host.
Types of Fiber: Soluble fiber forms a gel and is highly fermentable, while insoluble fiber adds bulk and promotes regular bowel movements.
Malabsorption Causes: Issues like enzyme deficiencies (e.g., lactose intolerance) or SIBO can cause normally digestible carbs to reach the colon.
Malabsorption Symptoms: Excess fermentation due to malabsorption leads to symptoms such as gas, bloating, diarrhea, and abdominal pain.
Gut Health Importance: Maintaining a balanced diet with diverse fiber sources supports a healthy gut microbiome, which is essential for overall health.

The Intestinal Journey of Carbohydrates

Most carbohydrates, such as simple sugars and digestible starches, are broken down by enzymes in the mouth and small intestine into simple sugars like glucose, fructose, and galactose. These simple sugars are then absorbed into the bloodstream for energy. However, not all carbohydrates are processed this way. Dietary fiber and resistant starch are designed to bypass this enzymatic digestion entirely and continue their journey to the large intestine, or colon.

The Fermentation Process: A Symbiotic Relationship

When these undigested carbohydrates reach the colon, they become a feast for the trillions of bacteria that make up your gut microbiome. This is a symbiotic relationship: the bacteria get to feed, and in return, they produce compounds that offer significant health benefits to the human host. This process is known as fermentation, and it's a normal and healthy part of digestion.

The fermentation of these resistant carbohydrates by the gut bacteria produces a number of byproducts, including gases and short-chain fatty acids (SCFAs). The main SCFAs produced are acetate, propionate, and butyrate.

The Benefits of Short-Chain Fatty Acids

Butyrate: This is a preferred energy source for the cells lining the colon (colonocytes). It helps maintain the integrity of the gut lining, reduces inflammation, and may play a protective role against colon cancer.
Propionate and Acetate: These SCFAs are absorbed into the bloodstream and travel to the liver and other tissues. Propionate can help reduce cholesterol synthesis, while acetate is used for energy by various cells, including muscle cells.

Soluble vs. Insoluble Fiber

Dietary fiber is generally categorized into two main types: soluble and insoluble. Both are undigested by human enzymes but have different effects during their journey through the digestive system.


Feature	Soluble Fiber	Insoluble Fiber
Effect in Gut	Forms a gel-like substance by dissolving in water.	Remains mostly unchanged and adds bulk to stool.
Fermentability	Highly fermentable by gut bacteria.	Less fermentable; primarily serves as a bulking agent.
Digestive Impact	Slows digestion, which helps stabilize blood sugar and cholesterol levels.	Speeds up the movement of waste through the intestines, promoting regularity.
Sources	Oats, beans, lentils, peas, apples, citrus fruits, barley, psyllium.	Whole wheat, wheat bran, quinoa, brown rice, nuts, seeds, vegetable skins.

When Digestion Goes Wrong: Carbohydrate Malabsorption

Sometimes, even normally digestible carbohydrates like lactose or fructose are not properly absorbed in the small intestine. This is known as carbohydrate malabsorption and can be caused by several factors.

Common causes include:

Enzyme Deficiency: A lack of specific digestive enzymes, like lactase (causing lactose intolerance) or congenital sucrase-isomaltase deficiency, means certain carbohydrates aren't broken down.
Small Intestinal Bacterial Overgrowth (SIBO): An overgrowth of bacteria in the small intestine causes fermentation to occur too early in the digestive tract.
Intestinal Damage: Conditions like Celiac disease, Crohn's disease, or infections can damage the intestinal lining, impairing nutrient absorption.

In these cases, a much larger load of fermentable carbohydrates reaches the large intestine, overwhelming the system.

Consequences and Symptoms of Malabsorption

The fermentation of this larger-than-normal amount of carbohydrates leads to intensified symptoms.

Gas and Bloating: Excessive fermentation by gut bacteria produces large volumes of gas (hydrogen, methane, carbon dioxide), causing bloating, flatulence, and abdominal distension.
Diarrhea: The unabsorbed sugars create an osmotic load, which draws water into the intestines. This, combined with accelerated intestinal transit, results in watery stools.
Abdominal Pain and Cramping: The stretching of the intestines from gas and the accelerated movement of food can lead to discomfort and painful cramps.

Conclusion: A Balancing Act

In a healthy digestive system, the fermentation of undigested carbohydrates like dietary fiber is a crucial and beneficial process that nourishes the gut microbiome and produces health-promoting SCFAs. However, when malabsorption occurs due to underlying issues, the fermentation process can become problematic, leading to uncomfortable and disruptive symptoms. Focusing on a balanced diet rich in whole foods is key to supporting a healthy gut ecosystem, but consulting a healthcare provider is important if you experience persistent symptoms of malabsorption.

For additional information on different types of fiber, the Harvard T.H. Chan School of Public Health offers a comprehensive guide on their website, The Nutrition Source.

Frequently Asked Questions

The carbohydrates not fully digested by the body are primarily dietary fiber and resistant starches. Humans lack the enzymes required to break them down in the small intestine.

When gut bacteria ferment undigested carbohydrates, they produce beneficial compounds called short-chain fatty acids (SCFAs), as well as gases like hydrogen and methane.

SCFAs are metabolic byproducts of bacterial fermentation, including butyrate, propionate, and acetate. They serve as a primary fuel for colon cells, help reduce inflammation, and can be used for energy by the liver.

Soluble fiber dissolves in water, forming a gel, and is readily fermented, while insoluble fiber does not dissolve and acts as a bulking agent. Both are important for digestive health.

Symptoms of carbohydrate malabsorption include bloating, excessive gas, abdominal pain, and diarrhea. These occur because unabsorbed sugars and excess gas disrupt the digestive system.

Yes, some foods are more likely to contain undigested components, like high-fiber vegetables (e.g., corn, peas), seeds, and legumes. In cases of malabsorption, foods containing specific sugars like lactose or fructose can cause problems.

Noticing fibrous parts of food is generally normal. However, if it's accompanied by persistent diarrhea, unexplained weight loss, or blood in your stool, you should consult a doctor.