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Gut Fermentation: The Key to a Healthy Microbiome

When most people hear the word ‘fermentation’ in relation to the gut, they think of fermented foods. While fermented foods can be beneficial for a healthy gut, and will be covered in this blog, we are first going to discuss the natural fermentation process that happens in the gut and why it’s important.


What is fermentation in the gut?


Fermentation is defined as the breakdown of substances in the absence of oxygen and occurs in the colon, an oxygen-free environment where most of the gut bugs reside.

The substances fermented are compounds of the food you consume that are not digested in the small intestine, which happens simply because the body has no mechanism to break them down, or in the case of poor digestion or excess consumption. These substances are predominantly dietary fiber and protein, but also include other compounds such as fat and polyphenols.


Once they reach the colon, these substances are exposed to gut microbes. Some of these microbes are capable of breaking down these compounds, releasing energy and nutrients. This drives their metabolic activity and fuels their growth, supporting the overall microbial population and producing a range of by-products for our body or other microbes to use.


The type of by-product produced depends on the type of substance fermented. These by-products can be either:

  • Beneficial, such as short-chain fatty acids (SCFAs), vitamins (mainly vitamin K and B vitamins);

  • Benign or generally harmless, such as gases (carbon dioxide, hydrogen, hydrogen sulphide and methane); or

  • Potentially harmful, such as ammonia and phenols.


What are the benefits of fermentation?


Fermentation of carbohydrates and carbohydrate-based substances (such as fiber) leads to production of beneficial by-product, like vitamins and SCFAs, as well as providing fuel and promoting the overall abundance and diversity of the gut microbes that make up the gut microbiota.


The process of fermentation is essentially how the gut microbiota thrives, and in return, they reward us with nutrients.



The negative effects of fermentation


Fermentation in the gut isn’t always a good thing, and can result in unwanted symptoms, as well as potentially harmful by-products.


Protein fermentation

When protein is fermented in the large intestine, this can result in by-products like ammonia and phenols, which can be potentially harmful. However, this doesn’t mean you need to cut out protein completely to avoid this. Protein is an incredibly important macronutrient that most people could benefit from eating more of. The reality is, protein is usually consumed alongside carbohydrates, and this counteracts the possible detrimental effects of the by-products of protein fermentation.

When a person consumes protein with a source of fiber (i.e. vegetables and fruit) and/or resistant starch, the combination of compounds diminishes any negative effects of protein. 

Additionally, protein fermentation can occur due to poor digestion in the small intestine, as well as over consuming protein. Focusing on consuming 3-4 smaller portions of protein, as well as addressing any underlying digestive issues can help to ensure you’re not exposing yourself to the negative effects of protein fermentation.



GI symptoms from gut fermentation


Outside of protein fermentation, some people may experience uncomfortable GI symptoms like bloating, gas, constipation, diarrhea and pain as a result of carbohydrate fermentation.


There are a number of reasons this can happen, and I’m going to cover the top three, the first being that the fermentation is happening in the small intestine.

The role of the small intestine in the digestive process is mainly associated with breaking down foods and nutrient absorption. Gut microbes that ferment the remaining components of food reside in the colon, which in comparison to the small intestine, is a big space. Because one of the main by-products of carbohydrate fermentation is gas, fermentation in the small intestine can lead to uncomfortable symptoms like excess bloating and pain, because there simply isn’t much space to contain the gas, and there are a lot of bends and turns in the structure for the gas to get trapped.

Carbohydrate fermentation that occurs in the small intestine is associated with SIBO (Small Intestinal Bacterial Overgrowth), and typically presents as excess bloating, gas and pain that occurs soon after eating. If you suspect this is a problem for you, it is a treatable condition and getting tested is the first step. This is something I can assist you with, so please get in touch to learn more.


The second reason for unwanted symptoms caused by carbohydrate fermentation is overconsumption of fermentable dietary fiber. These symptoms are typically less severe than those we see in SIBO, and most people experience these from time to time. Eating large meals that contain lots of dietary fiber is going to make anyone temporarily bloated, simply because the more you eat, the more gas is produced. You can minimise these symptoms by reducing the volume of fiber in one meal. However, if it doesn’t cause pain or disrupt your daily life, you can choose to embrace the bloat, as it is a sign that you’re taking good care of your beneficial gut bugs!


Finally, carbohydrate fermentation can cause uncomfortable symptoms for those who are constipated. If you’re not excreting waste products fast enough via stool, you can end up with excess fermentation and excess gas. Additionally, backed up stool can dominate the space in the colon, leaving less room for gas to move through and be expelled, resulting in pain.

Keep in mind that constipation doesn’t simply mean that you haven’t had a poo for several days. You can poop every single day, and even multiple times and still be constipated. If your stools are dry, hard, or resembling rabbit poos, you’re likely constipated. If you’re needing to strain to have a bowel movement, or feel like it’s incomplete, you’re likely constipated. Addressing constipation is essential for you to reap the benefits of carbohydrate fermentation without discomfort.



The best foods to promote gut microbe diversity


Now that we’ve covered what gut fermentation is and why it’s important, let’s talk about the best foods to consume for beneficial fermentation to occur, and promoting gut microbe diversity.


Fermentable fibers

Fermentable fibers are the indigestible component of plant foods that nourish the beneficial microbes in the colon. The body itself cannot digest these foods, but our microbes can and we receive the benefits. They act as a fertilizer to promote the growth of the microbes that make up the gut microbiota. This is essential to the health and function of our immune system. However, you need the right gut microbes to digest these fibers.


If you have a history of gut problems, have taken a lot of antibiotics in your life, suspect you have SIBO, or don’t consume a lot of plant foods in general, suddenly increasing fermentable fibers in your diet may not be the best first step. Instead, addressing underlying imbalances and focusing on fermented foods first may be a better approach.


Fermented foods

Fermented foods are foods and beverages that have undergone controlled microbial growth and fermentation, and essentially contain probiotics.

Examples of fermented foods include yogurt, kefir, fermented cottage cheese, kimchi and other fermented vegetables, vegetable brine drinks, and kombucha tea.

Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, increasing the diversity of species, as well as having a positive effect on the immune system, metabolic health and inflammation.


The cheapest way to regularly consume fermented foods is to make your own. But this can be a barrier for most people as it is time consuming, so buying fermented foods is often easier. There are a lot of products available marketed as a fermented food, but not all foods that are made through fermentation contain live microorganisms when they reach store shelves or your kitchen table. For example, he dough that is used to make sourdough bread, is fermented by bacteria, but the microbes are destroyed during baking.


My tips for buying fermented foods:

-Only purchase products that are stored in the refrigerated section of your supermarket. Sauerkraut can often be found off the shelf, but this doesn’t have live microorganisms in it.


-Read the packaging and look for statements like “contains probiotics” or “contains live cultures.”


-Be wary of kombucha. There are a lot of brands out there that have little to no live microorganisms. Go for small batch brands or brew your own at home.


Probiotics vs fermented foods

While probiotic supplements can be useful for short-term use to target specific issues, fermented foods are a better long-term focus to both improve and maintain gut health. I never recommend taking probiotic supplements long-term as they contain huge amounts of bacteria that can result in excess lactic acid, which is associated with negative symptoms like brain-fog.


Final thoughts



  • Gut fermentation is both incredibly beneficial and potentially detrimental for your gut health and overall health.

  • Those with digestive issues often struggle as a result of fermentation, and addressing the reason behind this is essential to overcome symptoms, as well as enable them to consume a diet that promotes a healthy gut microbiome.

  • We need both fermentable fibers and fermented foods in our diet to promote a diverse population of microbes.



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