nutritionist discussing how you can digest best over online call

How You Can Digest Best: Breaking Down Food with Help from our Gut Microbes

Kristina Campbell, MSc

Written by: Kristina Campbell, MSc

Updated: May 6th, 2024

Even though it contains important nutrients such as fibre, vitamin C, and potassium, an apple sitting on the kitchen counter is useless to your body. To unlock its nutritional benefits, you need to pick it up, take a bite, and let your digestive tract do its work to break it down and absorb the nutrients into your bloodstream. 

Your digestive tract can’t do the entire digestive job independently. It needs help from the trillions of bacteria and other living microorganisms that live inside your digestive tract all the way from your mouth down to your colon and rectum. This collection of resident microorganisms, called the gut microbiome, is a key player in how you digest and use the food you eat. Also, some microbes within this collection have specialized jobs during digestion. 

Here’s a quick journey through your digestive tract, highlighting how specific bacteria in your gut microbiome help you digest your best. 

How Mouth Microbes Support our Heart Health  

Enzymes start digesting your food – especially the starchy components – the moment you put it into your mouth. But something special happens when bacteria in your mouth detect nitrates, which are substances found in foods that include (1): 

Upon encountering these nitrates, some bacteria in your mouth – for example, those in the groups Actinomyces, Haemophilus, and Veillonella – kick-start a chemical reaction that converts a portion of the nitrates to nitrites, and ultimately to a molecule called nitrous oxide (2).  

When nitrous oxide is absorbed through the gut and circulates in your bloodstream, it assists in keeping your heart healthy by relaxing the blood vessels and reducing blood pressure. Scientists believe that oral bacteria’s transformation of nitrates is why frequent use of antimicrobial mouthwash (which wipes out key bacteria) is linked with having a higher blood pressure. 

How the Bacteria in our Intestines Help us Digest Fats 

The small intestine is the digestive tract hub where most of your nutrients are broken down and absorbed into your body. For the most part, this feat is accomplished without special help – but when you eat a meal high in fat, your small intestinal microbes need to step in and assist. 

Select microbes in your small intestine, such as those in the family Clostridiaceae, multiply rapidly when you consume fatty foods. These bacteria collaborate with other bacteria in the small intestine to break down the fats (3). At the same time, some of the bacteria signal to the intestinal cells to package the fats and get them ready for absorption into your body. Without these bacteria, your body wouldn’t be able to digest a high-fat meal properly. 

Besides this main job of helping with fat digestion, small intestinal bacteria help break down certain carbohydrates. Bacteria from the groups Bacteroides and Prevotella create enzymes to digest some carbohydrates in the small intestine that your body is not otherwise equipped to break down. 

How the Large Intestine Creates Short-Chain Fatty Acids (SCFA’s) 

Perhaps the most famous function of bacteria in digestion is breaking down dietary fibre to produce molecules called short-chain fatty acids (SCFAs) in your large intestine.  

What are SCFA’s? 

SCFA’s are important acid molecules produced in the gut, which have receptors all over the body. Some SCFA’s stay within the gut to nourish the intestinal lining, and others get absorbed through the gut wall to circulate in the blood. 

Fermentable fibres in foods such as whole wheat, onions, and bananas, are not digestible by your body. So, during digestion, they pass right through the small intestine and make their way to your colon, where multitudes of bacteria are ready to break them down. The resulting SCFAs, created as by-products, provide energy to the gut cells and travel far and wide throughout your body to regulate metabolism, brain function, and more.  

Bacteria from the genus Bifidobacterium are particularly good at breaking down fermentable fibres. Starting when you’re an infant, these bacteria help you digest the complex sugars in breast milk (or the complex fibres that may be added to formula milk). Later in life, the overall proportion of bifidobacteria in your gut decreases, but these bacteria in your large intestine still work on your behalf, digesting the fermentable fibre you consume. Those who maintain higher levels of bifidobacteria at an older age tend to have better health and vitality. 

Bacteria in the large intestine help digest food by creating another important type of molecule: secondary bile acids. Initially, the liver makes molecules called primary bile acids, which are secreted in the small intestine and make their way to the colon (4). In that location, they encounter bacteria that convert them into secondary bile acids. These secondary bile acids are important because they not only facilitate the digestion and absorption of fats in the colon, but they also help you absorb cholesterol (which is required to build healthy cells) and some vitamins you need. 

Bacteria Help Digest Specific Foods 

Another important way bacteria help your digestion is by enabling you to break down certain foods you may have trouble digesting. Lactose intolerance is the best example of bacteria coming to the rescue for digesting a specific type of food. 

Normally the lactose in dairy foods is broken down by an enzyme called lactase, so the individual building blocks of lactose can be absorbed via the small intestine. However, individuals with lactose intolerance underproduce lactase, so a higher amount of lactose goes down to the colon. Bacteria there can break it down alright – but not without extra gases being produced and extra water being drawn into the colon. It’s a recipe for gas, bloating, and diarrhea. 

However, some colonic bacteria in the group’s lactobacilli and bifidobacteria have genes that allow them to break down and utilize lactose without the unpleasant side effects. If you consume these bacteria deliberately, you may be able to improve your tolerance of lactose. In a published scientific opinion, European regulators who examined the evidence determined that that live cultures in yogurt are effective for improving lactose digestion (5). 

Other food intolerances can occur if you don’t have the right colonic bacteria to digest them. Sorbitol, for example, is a specific type of carbohydrate called a sugar alcohol, which can cause diarrhea when it’s not adequately absorbed in the small intestine. A recent study found that sorbitol intolerance can be resolved (and the unwanted symptoms avoided) if certain bacteria are present: those from the class Clostridia, or certain beneficial strains of Escherichia coli (6). 

Wanted: Microbes to Help with Digestion 

As these examples show, successful digestion isn’t entirely your own job. It requires you to work as a team with the trillions of microbes that call your digestive tract home.  

So, how do you know if you have the right microorganisms in your gut to help digestion proceed smoothly? The best way to ensure these microorganisms are present is to aim for diversity in your gut microbiome. 

If you’re a generally healthy person, eating a variety of plant foods – at least 30 different types per week helps you maintain a diverse gut microbiome that’s equipped for good digestion. 

Eating more probiotics and more fermented foods are also good strategies for increasing the diversity of microbes in your gut. Remember that the microorganisms present in some fermented foods are not necessarily the same thing as probiotics – the types and amounts of microbes are unknown, so they can’t be guaranteed to give you a health benefit. Probiotics, on the other hand, are specific microbial strains and amounts that are tested and shown to give you a health benefit. Nevertheless, both probiotics and fermented foods can increase diversity in your gut. 

You can specifically look for probiotics that have been tested and shown to deliver specific benefits, such as better lactose digestion. Finally, daily exercise also appears to increase diversity within your gut – so get those microbes moving. 

The next time you eat an apple, remember the microbial magic that helps your body make use of all the nutrients. And know that you can support the process by keeping your gut microbiome diverse and thriving. 


  1. Sweazea KL, Johnston CS, Miller B, Gumpricht E. (2018), Nitrate-Rich Fruit and Vegetable Supplement Reduces Blood Pressure in Normotensive Healthy Young Males without Significantly Altering Flow-Mediated Vasodilation: A Randomized, Double-Blinded, Controlled Trial. J Nutr Metab.,1729653. doi: 10.1155/2018/1729653. 
  2. Morou-Bermúdez E, Torres-Colón JE, Bermúdez NS, Patel RP, Joshipura KJ. (2019). Pathways Linking Oral Bacteria, Nitric Oxide Metabolism, and Health. J Dent Res.,101(6):623-631. doi: 10.1177/00220345211064571. 
  3. Chang EB, Martinez-Guryn K. (2019). Small intestinal microbiota: the neglected stepchild needed for fat digestion and absorption. Gut Microbes,10(2):235-240. doi: 10.1080/19490976.2018.1502539. 
  4. Zeng H, Umar S, Rust B, Lazarova D, Bordonaro M. (2019). Secondary Bile Acids and Short Chain Fatty Acids in the Colon: A Focus on Colonic Microbiome, Cell Proliferation, Inflammation, and Cancer. Int J Mol Sci., 20(5):1214. doi: 10.3390/ijms20051214.  
  5. Scientific Opinion on the substantiation of health claims related to live yoghurt cultures and improved lactose digestion (ID 1143, 2976) pursuant to Article 13(1) of Regulation (EC) No 1924/2006 (2011). Available online: 
  6. Lee JY, Tiffany CR, Mahan SP, Kellom M, Rogers AWL, Nguyen H, Stevens ET, Masson HLP, Yamazaki K, Marco ML, Eloe-Fadrosh EA, Turnbaugh PJ, Bäumler AJ. (2024). High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota. Cell, 187(5):1191-1205.e15. doi: 10.1016/j.cell.2024.01.029. 

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