Short Chain Fatty Acids - Benefits for Gut Health, Immunity and Beyond

Affiliate Disclosure

short chain fatty acids SCFAs butyrate benefitsShort Chain Fatty Acids (SCFA’s) are byproducts of healthy gut microbes after interacting with dietary fiber.

In return, SCFA’s support immunity, mucosal health, leaky gut, inflammation, and probiotic benefits (1).

The main SCFA’s produced in the gut are butyrate, propionate, and acetate.

They are predominantly produced in the colon. SCFA’s can be found in other areas of the intestines and can circulate in the bloodstream to help support the liver, lipid balance, cell growth, energy production, and more.

Butyrate is the most frequently studied of the SCFA’s and is also a primary fuel source for colonocytes.

SCFA’s can also pass the blood-brain-barrier and affect the brain.

One potential benefit of SCFA’s for the brain is playing a potential role in appetite suppression (2).

More exciting, SCFA’s can train immune cells in the gut to fight autoimmunity in the brain (3). While brain inflammation tends to capture the attention, the immune training is not specific to the brain, and extends to immune responses across the entire body (4; 5; 6). 

Immune tolerance is why someone can be more susceptible to food or environmental allergies than others. A loss of immune tolerance is key to all autoimmunity and is why immune cells start to treat healthy cells as foreign or pathogenic (7; 8; 9).

SCFA’s, along with probiotics, play crucial roles in not only keeping the immune system strong, but also keeping immune cells smartly trained to minimize collateral damage from their efforts to protect you.

When you eat certain food antigens or are exposed to mold, pollen or man-made pollutants in the air or water - the immune system can see these as problems and initiate an immune response.

A poorly trained immune cell will inevitably engage in friendly fire on healthy cells. 

As your gut flora changes, the amount and ratio of SCFAs will also change.

Healthy production of SCFAs may help reduce the risk of gastrointestinal disorders, food allergy, inflammation, oxidative stress, immune disorders, cancer-promoting processes, and cardiovascular disease (10; 11; 12; 13; 14; 15; 16). 

Functionally, SCFAs may also support blood flow to the colon, mineral absorption, healthy intestinal pH, normal bile and cholesterol metabolism, and the motility of material passing through (17; 18). 

By promoting healthy intestinal pH, SCFAs provide antimicrobial and probiotic benefits as pH can dictate what types of bacteria are able to grow (19).

Leaky gut is when there are holes or gaps in the intestinal barrier and allows pathogens, toxins or food proteins to pass into the blood. This triggers immune activation - and is a key feature of how certain foods can trigger immune flare-ups in auto-immune sensitive individuals.

SCFAs help to reduce leaky gut directly by helping to improve the assembly of tight junctions and their reassembly following damage (20; 21; 22).

Leakiness of the gut is also largely improved as a secondary benefit to all of the other benefits discussed previously.

When gut health is disturbed, we lose the self-sustaining benefits of SCFA production and the whole system has more difficulty recovering.

It’s clear - the production of SCFAs in the gut is important to re-establish and maintain healthy gut function. The benefits extend far beyond the gut and positively influence the brain, weight management, energy metabolism, inflammation, immune health and more.

The Master Assembly Line of the Gut

gut metabolites benefitsThe gut is an assembly line with multiple departments. 

Within each department of the gut (stomach, small intestine, large intestine, colon) different workers are present that

  • Protect the “GI factory” from accidents and damage to its machinery (Gut-Associated Lymphoid Tissue)

  • Bind toxins (immunoglobulins)

  • Keep the assembly line moving (vagus nerve and motility)

  • Ferment food (probiotics) to extract and manufacture useful nutrients and metabolites from the material as it passes through.
The healthier the entire system, the more metabolites you’ll pull from the food you eat, the more efficiently you’ll get rid of wastes  - and the less collateral damage that’s experienced along the way.

Your gut is lined with receptors for these various metabolites and action on these receptors leads to a cascade of anti-inflammatory benefits across the body (23).

SCFA’s are among the most important metabolites produced in the colon at the end of the assembly line - and they work to help the entire “GI factory” work more efficiently long-term (24). 

So when SCFA’s are deficient - it becomes very difficult to re-establish a healthy working environment in the gut and immunity and metabolism can be thrown off-kilter.

At the very least, a deficiency in SCFAs will put much more strain on your needs for probiotic balance, flora diversity, prebiotic and fiber intake, and mucosal support. 

How to Boost Short Chain Fatty Acid (SCFA) Levels in the Body

By starving the body of SCFAs like butyrate, you’re starving the body’s ability to regulate intestinal health, immunity, inflammation, and proper cell growth and signaling. 

Here are some strategies to boost levels and the production of short chain fatty acids.

1.) Take SCFA’s Directly

While the goal is to restore gastrointestinal health and flora diversity, you can support butyrate and other SCFA levels directly with supplementation.

Pure Encapsulations offers Sunbutyrate Tg Liquid that can be used to help support butyrate levels. Apex Energetics offers Enterovite capsules which support butyrate, acetate, and propionate levels.

2.) Supplement with SCFA producing Probiotics 

Spore probiotics like Megasporebiotic help support levels of healthy bacteria in the gut - especially when probiotics are combined with prebiotics

Bifidobacteria predominate in the large intestine where the majority of food fermentation takes place. I use Trubifido (most commonly the PRO version) to support Bifidobacteria levels. Prebiotics will also support the growth of Bifidobacteria.

Bifidobacteria work synergistically with butyrate-producing bacteria and dietary and supplemental prebiotics to boost butyrate production (25).

A new supplement in development is Butyrate Ultra by Microbiome Labs. It contains Butyricicocci which directly supports butyrate production. Normally, Butyricicocci bacteria are unable to be supplemented because they are anaerobic and are killed by the presence of oxygen. 

Microbiome Labs is devising a way to supplement with the anaerobic bacteria by producing it in an anaerobic lab and encapsulating it prior to its exposure to oxygen. This technology will open the door to many strains of probiotic bacteria that we know to be healthy but could only promote with diet and supplemental prebiotics.

3.) Consume or Supplement with Prebiotics that Fuel SCFA-Producing Probiotics

SCFAs are produced when bacteria in the gut act on fiber and polysaccharides in the intestine. Ensuring dietary intake of fiber, plants, and herbs, as well as supplementing with outside fiber (26) will support SCFA production in the body.

I commonly supplement with Megaprebiotic, Sunfiber, Trufiber, and Biotagen, and introduce them slowly (mostly in that order over weeks/months) as intestinal health improves.

The order of introduction is reflective of client tolerance, and the types of bacteria each fiber type has the potential of promoting. Long-term, I take these interchangeably to keep the system guessing and fuel different types of beneficial bacteria.

Fiber is ultimately essential for optimal flora activity - but start low and work up systematically. If one formula is not tolerated even in small amounts, try a different fiber and come back to the original at a later time.

A poor tolerance to a formula may mean that inflammation and intestinal dysbiosis or overgrowth may still be high. It may also mean that someone took too much too soon.

Long-term, I recommend rotating products like these to continue to promote microbial and metabolite diversity in the gut and keep the system “guessing”. 

The more fuel types (diverse fibers and chemicals from food and supplements) you provide the body - the more plentiful and diverse metabolites the assembly line will produce. The more plentiful and diverse metabolites - the more diverse the situations the body can respond to optimally.

"Health" is the body's ability to respond to an ever-changing environment. Gut-derived metabolites are critical to help the body respond optimally.


Not all probiotics in the gut have been identified, and not all beneficial flora that produce SCFAs can be supplemented orally - the next best thing is to provide fuel for these bacteria in the form of diverse prebiotics and food phytochemicals.

It is best to start slowly and methodically any time you introduce new fibers to the diet - and the same generally goes for high-FODMAP foods and new probiotics.

4.) Eat the Rainbow: Eat colorful fruits and vegetables and provide diverse polyphenols and plant chemicals to support bacterial diversity and metabolite production.

By eating the rainbow, I'm certainly not talking about Skittles. I'm talking about powerful phytochemicals.

SCFA production is also promoted by the intake of polyphenols in the diet - which offer antioxidant, anti-inflammatory and prebiotic benefits.

Curcumin, bioflavonoids, EGCG from green tea, resveratrol, quercetin, Beta-glucan, and others are well-regarded in the literature for wide-reaching health benefits for the gut, immunity, and beyond.

Poor tolerance to polyphenols again may mean that inflammation is too high or there is a deficiency in the right microbe imbalance able to process the polyphenols appropriately.

Luckily - a key benefit of polyphenols is their anti-inflammatory properties and sometimes you need to experiment to find the right mix for you.

The gut mucosa can not repair itself at the same time it is inflamed. Polyphenols simultaneously cool this inflammation and allow probiotics, prebiotics, and the other benefits of polyphenols to work more effectively.

Megamucosa by Microbiome Labs contains a combination of mucosa-supporting amino acids, bioflavonoids and immunoglobulins. It was formulated specifically to help support mucosal lining health and inflammation. It has quickly became one of our most popular and clinically supportive products.

The intestinal mucosa cannot be “inflamed” and “healing” at the same time, and so these strategies work hand-in-hand with one another. 

Likewise, Megaguard by Microbiome Labs contains a novel mix of flavonoids from licorice. Flavonoids are a chemical subset of plant polyphenols that work to support stomach inflammation, provide antimicrobial support, promote mucosal health, and spur motility and gastric secretions when combined with ginger and artichoke leaf.

Be mindful of high fructose content of some fruits, and don’t be afraid to add fresh citrus zest (organic preferred) to home recipes to boost the polyphenol content of your food and add a burst of flavor too.

The Standard American Diet is full of colorless, packaged, and processed foods that leave out the fiber and rich plant chemicals that are necessary for optimal gut function. Sadly, a majority of dietary fiber in American diets comes from breads and pasta.

Gluten is known to cause leaky gut and inflammation - even in the absence of a true immune reaction. These symptoms are actually more likely to result in brain fog, sore joints, and other symptoms than they are likely to result in loose or constipated bowels, stomach pain, or intestinal discomfort!

When removing wheat, it will help soothe this inflammation and patch up holes in lining - but after removing wheat from your diet, you must add other sources of prebiotic fiber or chance creating other problems for yourself. 

I discussed some of the new research and the importance of eating prebiotic fiber while following a gluten-free diet here: New Reasons to Go Gluten Free for Long-term Gut and Immune Health - Why the Naysayers are Still Wrong.

Given the prevalence of wheat in American Diets - as well as the trendiness of gluten-free diets - and the seriousness of replacing the lost prebiotic fiber, I feel that article is one of the most important that I've written recently.

If autoimmunity, early aging, and loss of brain function are long-term concerns - I suggest a gluten-free diet - AND doing it "correctly".

5.) Maintain a Virtuous Cycle of Intestinal Health

Health in the gut is self-perpetuating once the ball is moving in the right direction.

By promoting healthy bacteria in the gut and reducing gastrointestinal inflammation, you’re promoting healthy SCFA production too in a self-perpetuating cycle. SCFAs help maintain mucosal health and an anti-inflammatory environment that good bacteria depend on in order to thrive.

Eating a diet that is increasingly diverse in plant fibers and countless plant chemicals is the key to maintaining this beautiful system long-term.

It can take some time to tolerate many foods again and I’ve explored a more complete model of healing the gut lining and adding probiotic and prebiotic diversity.

These strategies will all work together and can be personalized to improve levels of SCFA production in the gut.

By Alex Rinehart | December 21st, 2019| |

Shop Supplements

Dr Alex Rinehart

Most Popular