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Butyrate is a short-chain fatty acid made by the good bacteria in your gut, and its job is to regulate digestion and inflammation. This molecule is key to stopping leaky gut, which is often a root cause of autoimmune disease. Incorporating butyrate foods into your diet will support a robust microbiome and healthy gut, all while helping to keep inflammation under control. 

In this article we will be diving into the science of butyrate — what it does, how it builds and maintains a healthy gut, and its connection to autoimmune diseases (AD). We explain why fiber is so important, and which kinds are the best fuel for gut microbes to make butyrate. Incorporating these fiber-rich, butyrate foods in your diet is an easy way to reap all the benefits of this short chain fatty acid. 

What Is Butyrate?

Butyrate and butyric acid are often used to describe the same molecule, but they are slightly different in chemical structure. Butyrate is the conjugate base of butyric acid, meaning when you mix butyric acid with water, you get butyrate, and vice versa. Both molecules contribute to the science and benefits of what we refer to as “butyrate” in this article. 

Butyrate is a short-chain fatty acid (SCFA) that gut bacteria produce as a by-product of metabolizing prebiotics such as dietary fiber and resistant starch. SCFA are metabolites, meaning they are produced by the breakdown of certain foods and nutrients, and SCFAs perform several important jobs throughout the body. The gut microbiota’s incredible impact on our physical health is partly via all the metabolites they make. (Source)

Butyrate is produced in the colon and transported throughout the gastrointestinal (GI) tract. It’s extremely important for digestive system function, immune system regulation, and keeping inflammation in check. Many different autoimmune diseases are associated with low butyrate, which makes sense because this SCFA is a cornerstone of managing inflammation. (Source, Source)

What Exactly Does Butyrate Do?

Butyrate is continuously being researched for the full scope of its effects on the body but most of it is made in, and tends to stay in, the colon. Butyrate provides up to 95% of the fuel for the cells that make up the lining of the intestinal wall. These cells, called colonocytes, control bowel function and house a generous portion of the microbiome, making it essential that they work properly. Butyrate also aids the colon in water and electrolyte absorption to keep you hydrated and prevent diarrhea. It also works directly with immune cells, many of which have butyrate receptors. (Source, Source)

At the root of butyrate’s immunoregulatory superpowers is its ability to change the expression of genes through a process called histone acetylation. Not all of your genes are being expressed at the same time, and they often provide different and even contradictory instructions to your cells and body. Several mechanisms “choose” which instructions will be followed, one of which is histone acetylation — a process where tightly bound “inaccessible” DNA is unwound so it can be expressed.

Since your DNA is constantly telling your cells what to do and when, histone acetylation has a profound effect on GI function. Through this mechanism, butyrate stimulates cell death to prevent colon cancer, and reduces the oxidative stress and inflammation caused by toxins and harmful microbes passing through the colon. We’ll dive deeper into this later when we cover how butyrate (or lack thereof) is connected to autoimmune diseases. (Source

Health Benefits of Butyrate Foods

Butyrate’s benefits extend to the whole body. It increases the insulin sensitivity of your cells to keep your blood sugar levels normal. High blood sugar drives inflammation and can ultimately lead to cells becoming insulin resistant, which is a root cause of diabetes, obesity, polycystic ovary syndrome (PCOS), and potentially Alzheimer’s. So having good insulin sensitivity is a cornerstone of health and protecting yourself from damaging inflammation.

Research has found that people with type 2 diabetes have less butyrate-producing bacteria in their gut microbiome. Some of butyrate’s influence on gene expression also seems to impact heart health, specifically by preventing the deposit of fat in the walls of veins. Interestingly enough, multiple studies have found that people with cardiovascular diseases have fewer butyrate-producing enzymes and bacteria in their gut microbiome. (Source, Source)

How Is Butyrate Connected to Autoimmune Disease?

About 70% of your entire immune system is housed in your gut, so unsurprisingly many autoimmune diseases are connected to gut dysfunction and an unbalanced microbiome. This explains why digestive symptoms are so common for people with AD. In fact, ulcerative colitis, Crohn’s disease, and celiac disease result from immune system dysfunction directly in the small and large intestines. Other ADs, including lupus, Graves’ disease, Hashimoto’s disease, type 1 diabetes, and rheumatoid arthritis are connected to GI inflammation and often impact digestive function. (Source)

Before we get into how butyrate helps to regulate autoimmunity, here's a quick recap on the gut-immune axis: Both the small and large intestines are lined with just a single layer of cells (epithelial cells) that gatekeep the contents of your gut from the rest of the body. These epithelial cells are coated in a protective mucus that keeps toxins out while letting water and nutrients in.

Because they constantly come in contact with the microbes, allergens, and toxins passing through your system, epithelial cells easily become inflamed and may contribute to symptoms such as bloating, fatigue, brain fog, and joint pain. Excessive inflammation loosens the tight junctions that connect neighboring epithelial cells to each other so that toxins and microbes can pass into your body, causing leaky gut syndrome. Leaky gut has been identified as a root cause of autoimmune disease, so it's important to address it. (Source)

Butyrate supports digestive health by increasing production of protective intestinal mucus and decreasing intestinal permeability. A lot of the inflammation in your gut is driven by harmful microbes and allergens that the immune system responds and sometimes overreacts to. Butyrate both increases the production of antimicrobial peptides and also tamps down cytokine production, so that inflammation stays in check. This is especially important for people suffering from Crohn’s and celiac disease, which are caused by an immune system attack on the gut lining that damages the cells and mucus layer.

Autoimmunity occurs in part because regulatory T-cells that suppress the immune response don't work properly. Without the T-cells preventing the immune system from attacking itself, your risk of developing an AD or having a flare-up increases. Butyrate and other SCFAs made in the gut stimulate regulatory T-cell production, a critical process for shutting off these autoimmune responses. (Source, Source)

Butyrate and Irritable Bowel Syndrome (IBS)

Irritable bowel syndrome (IBS) is a condition that occurs when the nervous system doesn’t properly control intestinal movement, causing constipation, diarrhea, gas, bloating, and abdominal pain. If you have an autoimmune disease, you are even more likely to have IBS. This dysfunction is driven by a number of causes, including dietary FODMAPs, gut dysbiosis, and stress.

It’s also very common — an astounding 45 million people in the US struggle with IBS. Research confirms that people with IBS have fewer butyrate-producing bacteria in their gut, which makes sense given how important this molecule is for regulating digestive health. Both the constipation and the diarrhea caused by IBS damage the gut microbiome and drive inflammation. (Source, Source)

Butyrate has been extensively researched for its ability to support intestinal health by regulating bowel function and reducing the uncomfortable symptoms associated with IBS.​​ In a study done in 2022, those with IBS experienced clinically significant relief from symptoms when given a 150 mg dose of sodium butyrate twice a day for 3 months, with 93% of the participants wanting to continue taking sodium butyrate after the trial had ended. Butyrate was found to be effective at regulating bowel function and is now used therapeutically to manage IBS symptoms.​​ (Source)

How Do I Know If I Need More Butyrate?

If you're struggling with a chronic GI condition (e.g., Crohn’s, IBS, leaky gut) you could probably use some more butyrate. The standard American diet tends to be heavy in highly processed seed oils, grains, and refined sugars, which the body can’t use to make butyrate. In fact, constant exposure to these foods makes the gut more inflamed, and therefore more in need of butyrate. And if you tend to skip fruits and vegetables with meals, that’s another sign your microbiome could use more fuel to make butyrate.

There are many different symptoms of GI inflammation that often occur in conjunction with low butyrate. Some of the more common symptoms include: 

  • bloating 
  • diarrhea 
  • abdominal discomfort 
  • indigestion
  • irritable bowel syndrome (IBS)
  • joint pain 
  • brain fog 
  • inflammatory bowel disease (IBD) 

If you have symptoms of low butyrate, microbiome testing can help you better understand what's driving your inflammation. This test helps identify the root cause of gut dysbiosis on a microbial level, to better guide you through healing and recovery. Your WellTheory team can help you with microbiome testing and incorporating the results into personalized lifestyle changes that are effective and sustainable. 

What Are Butyrate Foods? 

There are two kinds of butyrate foods: foods that your microbiome can use to proliferate and increase the production of butyrate, and foods that directly supply your body with butyrate. Increasing butyrate levels is essential to healing gut dysbiosis, because butyrate:

  • seals the gut lining (and stops leaky gut)
  • regulates intestinal function 
  • lowers inflammation 
  • protects the microbiome and body from damaging bacteria and toxins

Our WellTheory Care Team can help you incorporate more butyrate into your diet while taking your lifestyle and autoimmune conditions into account. 


The easiest way to increase butyrate is by increasing dietary fiber, which feeds the good bacteria in your microbiome. It is estimated that 95% of Americans don't have enough fiber in their diet, and the foods most heavily marketed as “good fiber sources,” such as whole grain cereals, usually don’t contain nearly enough to be claimed as such. Fruits, vegetables, legumes, seeds, nuts, and some starches are good sources of fiber. Fiber-rich foods that you may already have in your kitchen include: 

  • raspberries 
  • lentils (to be avoided if in the AIP elimination phase)
  • chia seeds 
  • artichokes 
  • cruciferous vegetables (broccoli, brussel sprouts, cabbage, bok choy) 
  • coconut meat and coconut flour 


Resistant Starch

Resistant starches are carbs your body can’t break down into energy, but your microbiome can. Like fiber, they are used by gut bacteria to make butyrate. Foods such as rice, sweet potatoes, and quinoa contain a small amount, which you can increase by cooking and then cooling or refrigerating before eating. An easy way to do this is by prepping your starch for the week in advance and keeping it in the fridge until it's time to heat it and enjoy. Foods that are naturally high in resistant starch include: 

Note that while sourdough bread, oats, and legumes are not AIP compliant, they may be added back into your diet during the reintroduction stage. (Source, Source)


Prebiotics are any foods or substances that nourish gut microbes, so technically they include the fiber and resistant starches covered above. Inulin, a carbohydrate that is considered a prebiotic, is particularly useful at building up the microbiome and is only found in specific fibers and resistant starches. The more fuel you provide for the good microbes in your gut, the more butyrate that can be made. Prebiotic foods include: 

  • sunchokes
  • dandelion greens 
  • onions
  • garlic 
  • leeks 
  • chicory 


Butter and Ghee

Dairy has become somewhat controversial in the wellness community. Some people love their farmer’s market goat cheese, while others believe dairy is too inflammatory and should be avoided at all costs. Nevertheless, butter is one of the best sources of dietary butyrate. For those who are unable to tolerate dairy or are in the reintroduction stage of the autoimmune protocol, ghee is a good nutrient-dense, casein-free, and lactose-free option. Try buying grass-fed butter or ghee, as they contain higher levels of butyrate than standard butter. (Source)

The Bottom Line on Butyrate Foods

Butyrate is a gut health super molecule that is essential to keeping inflammation in check. It can only be made by the microbiome out of fiber and resistant starch, so it is important that you have the right sources of these foods in your diet. Eating more butyrate foods not only has anti-inflammatory effects, but is a great way to regulate bowel function, protect against leaky gut, and support your immune system. Talk with a health care provider or a Nutritional Therapy Practitioner if you have health conditions that may warrant consuming more butyrate-rich foods, and get guidance on how you can implement a butyrate diet.

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Butyrate Foods: How to Increase Your Butyrate Levels and Support Gut Health

Butyrate foods are essential for immune function and a healthy gut. Including butyrate foods in your diet can help reduce autoimmune symptoms.
Medically Reviwed
Medically Reviewed by
Dr. Danielle Desroche
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