Gut Health and Nutrient Absorption

by Rachel Stuck, RDN

All external surfaces of our bodies harbor microbes, but the most dense and functional microbes on our bodies are the ones that populate the gastrointestinal tract (GI tract). The bacteria in the gut are responsible for a wide variety of essential processes, including the harvest, digestion, and utilization of nutrients making the health of the good bacteria in the gut extremely important for adequate nutrient utilization and absorption. 

The gut microbiome is essential for the digestion and utilization of a variety of nutrients in the diet. From macronutrients including fat, protein, and carbohydrates, to micronutrients including vitamins and minerals, the bacteria in the gut play an important role in how well the body is able to breakdown and utilize these nutrients. (1)

Digestion and absorption of nutrients takes place primarily in the stomach and small intestine, but that is not to say that the large intestine, or colon, doesn’t also play a role in the digestion of nutrients. After food has passed through the stomach and small intestine, a majority of nutrients have already been absorbed, leaving a mixture of indigestible carbohydrates and proteins. The remaining carbohydrates and protein are fermented by good bacteria in the colon to produce short chain fatty acids (SCFA). (1) These fatty acids are then absorbed and utilized as fuel for various processes in the body.

Because SCFAs are the result of indigestible fibers and proteins being fermented by the bacteria in the gut, it is important to note that this process would not be able to happen if the diet did not provide foods with these nutrients. Fiber is only found in plant foods like vegetables, fruit, beans, legumes, and grains, which means that including a variety of fibrous plant foods is essential for the production and absorption of SCFAs. 

Bacteria in the gut also play an important role in the absorption of micronutrients. Most commonly known for the role it plays in the synthesis of vitamin B12 in the colon, gut bacteria also help facilitate the synthesis of thiamin, folate, biotin, riboflavin, and pantothenic acid. (2) Gut bacteria also play a role in helping the body meet its daily requirement of vitamin K. It is estimated that the gut microbiome contributes about half of the body’s daily vitamin K requirement. (2) 

Maintaining a healthy gut is critical for proper nutrient synthesis and absorption. Without a balanced microbiome, nutrients found in the diet will not be fully broken down and utilized by the body. A diet rich in fiber-rich plant foods, protein, healthy fat, and fermented foods and low in high-sugar, overly processed foods will help support a healthy gut and ensure optimal nutrient absorption and utilization.

About the Author

Photo: Rachel Stuck, RDN

Registered Dietitian Nutritionist Rachel Stuck has a background in culinary arts and nutrition counseling. Rachel takes a positive approach to nutrition: she avoids recommending restrictive diets and instead focuses on helping people choose foods that promote health and well-being. She is passionate about empowering and assisting Ixcela members as they develop their unique, gut-healthy lifestyles.

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Interested in learning more about Ixcela? Check out Ixcela’s microbiome test, personalized nutrition and fitness plans, and other tools to help you optimize your health.


  1. Krajmalnik-Brown, Rosa et al. “Effects of gut microbes on nutrient absorption and energy regulation” Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition vol. 27,2 (2012): 201-14.
  2. Morowitz, Michael J et al. “Contributions of intestinal bacteria to nutrition and metabolism in the critically ill” Surgical clinics of North America vol. 91,4 (2011): 771-85, viii.