The Incredible Health Benefits of Short-Chain Fatty Acids in the Digestive System

Your microbiome plays a crucial role in immune function, metabolism, and even the gut-brain connection. And one of the most important aspects of gut health is the balance of short-chain fatty acids (SCFAs). These nutrients aren't just fats however. SCFAs are produced by gut bacteria, and they play a vital role in everything from glucose metabolism to protecting your nerve cells. In this blog post, you'll learn the incredible health benefits of SCFAs in the digestive system, and how you can maximize your intake. We'll also talk about what leads to reduced levels of SCFA and why that's a problem for our modern-day microbiome.

Learn more about conditions we treat: Leaky gut

What are short-chain fatty acids?

Short-chain fatty acids are made when beneficial gut bacteria break down dietary fiber as it travels through your digestive tract. This occurs in a process known as fermentation. Fermentation yields a number of different health-supporting compounds such as vitamins, proteins, and fatty acids.

Short-chain fatty acids are called such because they have 6 carbon atoms that make up part of their chemical structure. There are also medium- and long-chain fatty acids which have different functions within the body.

Up to 95 percent of SCFA are made up of 3 types:

  • Butyrate
  • Acetate
  • Propionate

Read: Superfoods for Your Microbiome

SFCA function and benefits

Short-chain fatty acids are the preferred fuel source for the cells in the human gut microbiome. This is important as these cells play a vital role in gut barrier function and immune regulation.

SFCAs also have anti-inflammatory effects, which is beneficial given that inflammation is at the root of many chronic diseases (1). 

Butyrate, in particular, has been shown to be protective against colorectal cancer (2). This is likely due to the fact that butyrate can inhibit the growth of cancerous cells and induce cell death (apoptosis).

Short-chain fatty acids have also been shown to reduce diarrhea symptoms, which may be beneficial for individuals with digestive health issues like IBS-D.

Learn more about gut health at CentreSpringMD

Short-chain fatty acids in the gut


Many studies have shown that butyrate, one type of short-chain fatty acid, can act as an anti-inflammatory agent. Several human and animal studies reported that it inhibits proinflammatory cytokines IFN-γ, TNF-α, IL-1β, IL-6, and IL-8, whereas it increases anti-inflammatory cytokines IL-10 and TGF-β (3). 

Further studies also showed that butyrate is capable of activating PPAR-γ, a hormone receptor whose activation reduces intestinal inflammation. This receptor is thought to play a role in the development of irritable bowel syndrome (IBD) (4). 

Leaky gut

The barrier function of intestinal tissue is the body's first line of defense, allowing water and nutrients in, but keeping harmful pathogens out. Short-chain fatty acids are known to repair and enhance the epithelial cells that make up the body's intestinal barrier (5).  

For example, SCFAs upregulate the expression of specialized peptides, and a molecule known as mucin 2 (MUC2), which protect and repair intestinal mucosa. While it may not sound like the most glamorous function, the presence of this mucus in the intestinal barrier is exactly what protects the human body against invading pathogens (6,7). 

Furthermore, butyrate modulates the expression of tight junction proteins to minimize intestinal permeability.

Immune function

SCFA are the preferred energy source for many gut cells, including macrophages and dendritic cells. These are immune cells that play a crucial role in gut health by modulating the inflammatory response.

Butyrate has also been shown to increase the production of regulatory T cells (Tregs) (8). Tregs are a type of white blood cell that helps to keep the immune system in check by suppressing excessive inflammation.

SCFA also support immune function by (9):

  • Influencing immune cell migration and function between cells. 
  • Cleaning up old or damaged cells in the gut lining

Related: Heal Your Gut to Improve Immune Function & More

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SCFA improve metabolism, and may help you lose weight

A significant factor for increased body weight in the general population is poor blood sugar control, or insulin resistance. Recent animal studies have shown that a healthy concentration of SCFA alleviates diet-induced obesity and insulin resistance (10). 

SCFA also influence how other nutrients are absorbed in the body. This may support a healthy metabolism, and lead to more sustainable weight loss. 

Researchers attribute this to the secretion of gut hormones glucagon-like-peptide 1 (GLP-1) and Peptide YY (PYY) in response to SCFA. These hormones can help reduce your appetite and promote fat-burning (11). 

SCFAs regulate the gut-brain axis

The gut-brain axis is a complex system that includes the gut microbiota, the enteric nervous system (ENS), and the central nervous system (CNS). This system is responsible for communication between the gut and the brain.

SCFA mediate communication between the gut and the brain through the various channels, such as:

  • The Vagus nerve
  • Hormones and the endocrine system
  • Neurotransmitters

Dysregulation of the gut-brain axis and/or poor gut health has been linked to several neurological disorders, including autism spectrum disorder, anxiety, and depression.

Acetate and the other SCFA have been shown to modulate the gut-brain axis by influencing the production of neurotransmitters, such as serotonin and dopamine (12)

They also play a critical role in the development and function of microglia, a type of immune cell designed to protect your brain and spinal cord.

What causes low SCFA levels?

Generally, low microbiome biodiversity results in lower short-chain fatty acid production potentials. And as modern microbiome diversity continues to decline, so do important by-products like protective fatty acids. In individuals with decreased microbial diversity, there are less bacteria capable of producing SCFA.

Dietary fiber is the primary food source for gut bacteria. Therefore, a diet low in fiber can lead to decreased SCFA production. In addition, processed foods and antibiotics can also disrupt gut bacteria and reduce short-chain fatty acid levels.

Western diets high in processed fats, refined carbohydrates and sugars, and low in fresh foods and fiber are associated with reduced microbial health and diversity, an imbalance of the gut ecosystem, and disease (13). 

Certain medical conditions are associated with low butyrate levels. These include inflammatory bowel disease (IBD), Crohn’s, celiac disease, and food allergies.

Read: How to Repair a Leaky Gut

SCFA and their role in MS

Recently, SCFAs have shown some promise in the treatment of multiple sclerosis (MS), a chronic disease affecting the CNS and characterized by degradation of the myelin sheath (demyelination) that protects nerves. 

Poor gut health and low microbial diversity resulting in a lack of SCFAs was found to increase this degradation process, leading to disease progression. Supplementation with one type of SCFA, butyrate, was found to actually help repair the myelin sheath (14). Reversing demyelination in MS patients would slow disease progression, reduce symptoms, and drastically improve quality of life.

Microbiome diversity and the resulting presence of SCFAs have been found to directly impact not only gastrointestinal health, but also neurodegenerative and inflammatory diseases. 

Related: Does Alzheimer’s Actually Begin in the Gut?

Foods to boost SCFAs

You can increase SCFA in your gut by consuming foods that increase your body’s production of them, or by taking supplements. Your digestive system ferments the fiber to generate SCFA. Therefore, a diet rich in fiber is important for gut health and the production of SCFA.

Foods that are great for your gut include:

  • Fermented foods like yogurt, kimchi, and sauerkraut
  • Raw honey
  • Apples
  • Pears 
  • Acacia fiber

Learn more: Where Do I Find Prebiotic Fiber?

Resistant starches are another type of important fiber for gut bacteria. This kind of starch is resistant to digestion, meaning more of it is available for the good bacteria in your colon. From there, these beneficial bacteria can ferment it and produce beneficial by-products like butyrate and propionate. Some of the best sources of resistant starches include:

  • Green bananas (also available in powdered supplement form)
  • Raw plantains
  • Cooked then cooled rice or potato
  • Legumes 

Include a variety of fruits, vegetables, whole grains, and legumes in your diet to increase the amount of fiber you consume. 

What about butyrate supplements?

Butyrate supplements are available in many health food stores and online. Butyrate or butyric acid supplementation has shown some promising results, particularly in those struggling with IBS, but more research is needed to determine whether or not it’s a truly effective solution. 

Most people are likely better off increasing intake of foods that support a healthy gut microbiome, thereby naturally increasing SCFA production. Butyrate supplements are usually absorbed before they reach the colon, meaning all the benefits for intestinal cells are no longer present.

Browse all digestive support supplements in the shop.

For more SCFA Focus On Balancing Your Microbiome

Without the right balance of bacteria, your body won’t be able to properly break down fiber or produce SCFAs.

  • Give gut bacteria a boost with a daily probiotic like HiFlora-50.
  • Eat a balance diet with a variety of vegetables, fruits, minimally processed grains, and legumes to increase dietary fiber
  • Try prebiotic fiber such as acacia fiber, which is a soluble fiber that gut bacteria ferment to produce SCFAs.
  • Include fermented foods like kimchi, yogurt, and sauerkraut in your diet for gut-healthy probiotics

Short-chain fatty acids are an important part of gut health. By including a variety of gut-healthy foods in your diet, minimizing environmental toxins, and living an overall healthy lifestyle, you can help increase SCFA levels and improve gut health.


  1. https://academic.oup.com/advances/article/9/1/21/4849000
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6566851/
  3. https://pubmed.ncbi.nlm.nih.gov/25234148/
  4. https://pubmed.ncbi.nlm.nih.gov/16905700/
  5. https://pubmed.ncbi.nlm.nih.gov/26491121/
  6. https://pubmed.ncbi.nlm.nih.gov/12970137/   
  7. https://pubmed.ncbi.nlm.nih.gov/22797568/ 
  8. https://www.frontiersin.org/articles/10.3389/fnut.2022.878382/full
  9. https://pubmed.ncbi.nlm.nih.gov/20823773/
  10. https://pubmed.ncbi.nlm.nih.gov/27528227/ 
  11. https://academic.oup.com/advances/article/9/1/21/4849000 
  12. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005631/ 
  13. https://asm.org/Articles/2019/November/Disappearance-of-the-Gut-Microbiota-How-We-May-Be 
  14. https://jneuroinflammation.biomedcentral.com/articles/10.1186/s12974-019-1552-y 


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