Gut Microbes—They Digest What You Can’t

Over the course of a lifetime 60 tons of food pass through the digestive tract.1 Carbohydrates, fats, and proteins—the macronutrients—are broken down into smaller parts—sugars, fatty acids, and amino acids—with the help of digestive secretions, like hydrochloric acid (HCl), and digestive enzymes. In an average healthy individual, about 85 percent of carbohydrates, 66 to 95 percent of proteins, and all fats are absorbed before digestive contents enter the large intestine.2 Yet, the non-digestible carbohydrates and proteins make up between 10 and 30 percent of total energy absorbed from the digestive tract. How is this possible?

The gut bacteria make it possible. In the large intestine, gut microbes ferment starch, sugars, fibers, and mucins into short-chain fatty acids and gases. Multiple factors affect how much and which SCFAs and gases are produced. These factors include age, diet, gut microbial composition, pH of the colon, and gut transit time (how long it takes food to travel through the digestive tract—in constipated people gut transit time is longer).

Carbohydrates are particularly important nutrients when it comes to gut microbes because carbs provide nutrients to the host (that’s you) and to the gut microbes. Non-digestible carbohydrates (otherwise known as fiber) are delivered to the colon and fermented by microbes. The SCFAs produced during this process—mainly acetate, propionate, and butyrate—are used to fuel intestinal cells (butyrate), are transported to the liver for energy production or cholesterol synthesis (propionate and acetate), or remain available in the blood as an energy source (acetate).2

Short-chain fatty acids make up about 6 to 10 percent of total energy absorbed from the diet. While this may not seem like much, the amount of energy absorbed from the colon, and how that energy is used, is an active area of research that is uncovering the effects of the gut microbiota on metabolic conditions such as obesity and insulin resistance. I’ve blogged about this gut connection to childhood obesity.

In yet another recent gut microbe study published in the PLoS One journal, researchers investigated the carbohydrate degradation activity of the microbiome throughout the body and concluded, “Digestion in the gut appears highly specialized for the digestion of carbohydrates.”3

It may seem obvious that gut bacteria are specialized to break down carbohydrates, but one interesting finding of the study was the ability of oral bacteria to produce, “a hitherto underestimated large range of enzymes to initiate plant polysaccharide breakdown as indicated by the presence of cellulases, hemicellulases, and pectin hydrolases.” It was previously thought that carbohydrate-digesting enzymes found in the mouth were secreted in saliva. Now we know our bacteria, even in the mouth, play an important role in digestion beginning in the mouth.

We are only beginning to scratch the surface of what can be known about the human microbiome, but one thing is for sure: We are a super-organism living in harmony (or disharmony in the case of poor health) with our inhabitants (our microbes). It is truly a humbling learning experience to know we are not as in control as we once thought.


  1. S. Bengmark, “Ecological control of the gastrointestinal tract. The role of probiotic flora.” Gut. 1998 January; 42(1): 2–7.
  2. R. Krajmalnik-Brown, et al., “Effects of gut microbes on nutrient absorption and energy regulation.” Nutr Clin Pract. 2012;27:201–214.
  3. B.L. Cantarel, et al., “Complex carbohydrate utilization by the healthy human microbiome.” PLoS ONE. 2012;7(6):e28742.
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