Short-Chain Fatty Acids: Your Shortcut to Better Health
“Happiness is always the happy result of something more fundamental.”
– Buddhist proverb
When it comes to creating good health, all roads lead to the microbiome. What was unknown in my childhood and little known even in my children’s childhoods is thankfully now becoming common knowledge: that a healthy microbiome is the foundation of good health. Your gut microbiome is the living interface between your internal body and the world you live in. There’s no escaping its impact – there’s only shaping and sustaining it with the foods you eat and the way you live.
Back in high school, you may have learned about the colon merely as an organ of elimination. It absorbs water and pushes solid waste from your body. Perhaps you also learned that it plays a role in eliminating or reabsorbing cholesterol. Little was it known back then that the colon is the matrix of the microbiome – the precious cauldron from which all health conditions unfold. Like the soil-food web in the forest, the human gut houses a hidden community of living microbes, more intricate and numerous than we can ever imagine. Its many activities include digestion – that is, cellular breakdown, absorption, and exchange; nutrient sensing and signaling; hormone secretion; enzymatic activity; electrochemical impulses; and more. If this vital ecosystem is dysregulated, deficient, or damaged, all kinds of downstream effects may ensue, from IBS to arthritis, from autoimmune conditions to cancer, from depression to dementia – in short, the many diseases and disorders that are so common today.
Conversely, a healthy gut is tantamount to a healthy body, and along with it, a happy brain. The gut-brain axis is now well established as a bidirectional signaling pathway that connects the two, and plays a direct role in cravings, energy, mood, immunity, and more. Similarly, the gut-skin axis is well understood as the link between what you eat and what shows up on your skin. Indeed, we could draw an axis from the gut to nearly every system in the body – including the immune system, which is largely produced in the gut.
That’s a lot of activity! Your internal ecosystem holds a great deal of power to do harm or good. How can you create a healthy microbiome, and leverage its power to your advantage?
To answer these questions, let’s look first at the lining of the colon, and then at its contents.
Consider your Colonocytes
Colonocytes are the epithelial cells that line the inner surface of your colon, or large intestine. These are highly active cells that consume a great deal of energy in order to function. Colonocytes absorb nutrients and water, and play a key role in mineral balance that directly regulates electrolytes, which in turn affects kidney function, heart rhythms, pH balance, blood pressure, and nerve impulses. These hard-working cells also detect microbial signals from gut bacteria, and produce signaling molecules of their own. They communicate with immune cells deeper in the intestinal wall, distinguishing beneficial microbes from pathogens. They help train the mucosal barrier between your gut and underlying tissues. They act as cellular gatekeepers, forming tight junctions which regulate what passes through the gut barrier into your bloodstream. If this barrier is functioning well, it prevents undigested food, harmful bacteria, bacterial by-products or endotoxins, and other illicit substances from entering the bloodstream.1 If these junctions become weak, intestinal permeability or “leaky gut” may result. Leaky gut may lead to autoimmune disorders, as the immune system interprets these foreign substances as a threat, and in attempting to eliminate them may attack your own tissues as well.
With all the many roles your colonocytes play, it’s no wonder they burn as much 70% of the energy of your basal metabolism (the energy your body needs to sustain basic life functions while at rest). Where do they get all this energy?
You might think it’s in the food you eat, and that’s certainly true – but there’s a hidden link, for it’s not the food itself that energizes your colon cells, but its fiber – and not even the fiber itself, but the fermented by-products of that fiber. These metabolites (products of metabolic processes) are known as short-chain fatty acids (SCFAs) or post-biotics, and they’re produced by those hidden heroes in your gut – your internal community of gut bacteria.
What are SCFAs?
The term “short-chain fatty acid” originates from its chemical structure, describing a carboxylic acid with a tail, or chain, of fewer than six carbon atoms. Biochemically, SCFAs are critical because they regulate immune system homeostasis, act as crucial signaling molecules along the gut-brain axis, and serve as the primary energy source for colonocytes.
The most common SCFAs are butyrate, acetate, and propionate. These friendly fellows are hard at work in your intestinal lumen, fermenting every form of fiber you eat, including certain prebiotic liquids, such as green tea, breast milk, olive leaf and mushroom extracts, and certain herbal infusions. SCFAs serve as the primary food source for colonocytes, supporting their growth, maintenance, functioning and repair; and thereby enhancing your overall intestinal integrity. By contrast, lack of SCFAs are correlated with constipation, obesity, and depression. SCFAs may increase concentrations of GLP-1 (which regulates appetite, the active ingredient in weight-loss drugs such as Ozempic), PYY (chemical messengers that suppress appetite, slow digestion, and help manage blood sugar levels), and leptin (the hormone that makes you feel satiated). SCFAs are also known to increase insulin sensitivity, suppress gluconeogenesis (the production of glucose within the liver), and slow down lipogenesis (fat production), shifting the body toward fat oxidation (weight loss) instead. Acetate even enhances the benefits of exercise by activating glucose transport independent of standard insulin pathways – in other words, delivering energy to your muscles during intense exertion without any insulin at all. This remarkable biochemical pathway is literally a shortcut for glucose to enter your cells – and a valuable one, too, which keeps blood sugar down and thereby maintains steady metabolism, reduces systemic inflammation from excess insulin, and lightens the load on your pancreas. SCFAs therefore play a significant role in preventing or even reversing diabetes – as well as the downstream effects of diabetes, which may include just about any chronic inflammatory condition or disease.
“SCFAs have many health benefits, such as anti-inflammatory, immunoregulatory, anti-obesity, anti-diabetes, anticancer, cardioprotective, hepatoprotective, and neuroprotective activities.”2
Sound too good to be true? The list goes on. SCFAs have also been shown to increase the absorption of calcium and magnesium, reduce blood pressure, strengthen the blood-brain barrier, down-regulate cancer cell proliferation, and attenuate cardiac dysfunction. Butyrate in particular influences epigenetic signaling in mast cells, basically flipping off the genetic switches that trigger allergic responses. This epigenetic signaling is also known to suppress the growth of colorectal cancer.3 Equally impressive, propionate travels to the liver to inhibit cholesterol synthesis and regulate gluconeogenesis. By contrast, insufficient SCFAs are associated with cirrhosis of the liver; whereas their abundance constitutes a treasure trove of detoxifying compounds.4 Emerging research is even exploring the potential of microbiome-targeted strategies for treating asthma via the “gut-lung axis.”5
Even your bone density may be enhanced by SCFAs!
“Move over calcium, vegetable fiber is a dietary element that is KEY to bone health. SCFAs acetate, propionate, and butyrate . . . produced through microbial fermentation of non-digestible dietary fiber . . . significantly increase bone mass. Acetate inhibits osteoclast numbers in a T-cell- and B-cell-dependent manner, while propionate and butyrate prevent bone loss by decreasing osteoclast number.”6
Cultivating SCFAs
Cultivating short chain fatty acids in your gut is like creating a beautiful inner garden. You are the garden bed. Soluble and insoluble fermentable fibers serve as the soil – premium substrate for gut microbiota to synthesize SCFAs. Examples of these fibers include:
Inulin and Fructooligosaccharides (FOS): Found in garlic, onions, leeks, and chicory root. They strongly stimulate Bifidobacteria, primarily yielding acetate and butyrate.
Resistant Starch: Found in green bananas, legumes, and cooked, chilled potatoes (as in potato salad). Resistant starch is the premier driver of butyrate production by feeding bacterial strains such as Roseburia and Faecalibacterium prausnitzii. The latter is known as the “king” of probiotic bacteria, with numerous benefits for human health (see my article Life As A Holobiont for more on this subject).
Oats and barley: These viscous fibers contain grain-based beta-glucans that slow gastric emptying and undergo fermentation to maximize overall SCFA volume. (Note: gluten in barley may outweigh its benefits for the gut; this is an individual decision depending on your diet and health goals. See my article Getting Granular About Gluten for more on this subject.)
Pectin: Abundant in apples, citrus fruits, and carrots. It is highly fermentable and heavily favors acetate and propionate synthesis.
Fiber from vegetables – especially leafy greens, cruciferous vegetables, and seaweed – is generally superior to fiber from grains and fruits,7 because it offers diverse structural carbohydrates (such as cellulose and inulin) alongside a dense concentration of polyphenols. This combination provides a varied "menu" that sustains a wider, more robust population of SCFA-producing gut microbes than the more uniform fiber types found in grains and fruits.
Mushrooms contain a highly specific matrix of fibers that trigger SCFA generation, including fungal beta-glucans – structural polysaccharides that act as a slow-burning food source for gut microbes, spiking overall SCFA production. Mushroom cell walls are made of chitin, a tough, insoluble fiber that resists digestion in the stomach and small intestines. Upon reaching the colon, chitin and fungal beta-glucans gradually degrade directly into acetate. Mushrooms also contain trehalose (a fungal sugar that mushrooms synthesize from glucose derived from plants and trees) and alpha-glucans – soluble carbohydrates that are rapidly fermented in the upper colon, providing quick energy to your precious colonocytes. This fermentation also provides a biochemical bridge by enabling the proliferation of beneficial, SCFA-producing bacteria such as Bacteroides, Bifidobacterium, and Lactobacillus.8
A low-acid diet also helps your colon produce SCFAs. One study indicated that low colonic pH value promotes butyrate production and increases populations of butyrate-producing bacteria.9 This means reducing or eliminating acid-producing foods in your diet – most notably sugar, alcohol, and ultra-processed foods. Find lists of acid-producing foods online, such as here. How do you know whether to reduce or eliminate these foods? That depends on your health goals and the state of your microbiome. (See my article Less Bad, More Good for more on this subject.)
Protecting the integrity of your gut lining is also important. Foods containing mucilage are beneficial, such as okra, chia seeds, flax seeds, fenugreek seeds, kelp, irish moss, aloe vera, slippery elm, psyllium seed, and herbal infusions of marshmallow root, linden flowers, violet leaf, and comfrey leaf. Avoid foods that degrade the delicate mucosal gut lining – most notably gluten (whether you are gluten-intolerant or not), as well as carrageenan, guar gums, NSAIDs, antacid medications, artificial sweeteners, alcohol, soda, and ultra-processed foods (chips, crackers, cookies, candy, fries, granola bars, and other junk foods).
Human breastmilk contains oligopolysaccharides, a prebiotic fiber that feeds butyrate. This is crucial for establishing a healthy microbiome in infants. The probiotic bacteria that ferments it, Bifidobacterium infantis, comes from the mother’s birth canal. Babies born by C-section may receive this crucial bacteria by means of a vaginal swab from the mother, or as a supplement.
SCFAs are produced endogenously, and therefore cannot be prescribed as pills or taken as supplements. Supplements that claim to provide butyrate really just contain the raw materials that help your body produce it. These include probiotic bacteria such as Akkermansia muciniphila10 that helps strengthen the gut lining – and like mushroom fiber, also jump-starts other strains that produce SCFAs – and prebiotic fiber, such as inulin, to feed those bacteria. Adding these supplements to your diet is like planting seeds in a garden. It’s up to you to enrich the soil. If it has no nutrients or the seeds don’t get sufficient water or sunlight, nothing will grow. Similarly, if your diet includes gut-degrading foods such as refined sugar, artificial sweeteners, inflammatory oils, pesticides, herbicides, preservatives, alcohol, antibiotics, mouthwash, painkillers, antacid medication, or chemical additives – these supplements cannot serve you well.
Probiotic supplements are currently not regulated, so any claims you see on the label are questionable. Some strains must be cultivated anaerobically, and require special capsules to prevent exposure to oxygen. Fermented foods – yogurt, kefir, kimchi, sauerkraut, miso, natto, tempeh, and kombucha – are a superior source of probiotic bacteria. Your goal is to consume two or three types every day.
How do you know if you have SCFAs in your gut? Lack of symptoms is the first sign – that is, smooth digestion. But you don’t have to have digestive issues in order to suffer the far-flung effects of a dysregulated gut. Insomnia, depression, anxiety, and brain fog may be the result, or eczema, psoriasis, or acne. SCFAs can cross the blood-brain barrier, influencing neuroinflammation and the production of neurotrophic factors. For better or worse, these short-tailed molecules are the means by which nutrition shapes your health.
“The role of SCFAs in human health and diseases has become a research hotspot.”
SCFAs are the happy result of a fundamentally healthy diet. This short-cut to better health takes time to establish, and mindful choices to sustain – but once in place, it enables you to bypass many of the chronic diseases that are commonly believed to be the result of genetics, or just plain bad luck. We now know better. The good news is you have far more agency over your health than you realize. It’s a lifelong project well worth pursuing. After all, the Panama Canal wasn’t built overnight – it took over ten years and more than 75,000 workers from many countries. But once constructed, the canal bypasses 8000 nautical miles of travel by sea. Imagine a similar long-term project in your body, with an equally diverse community of living organisms, working together to bypass the long and arduous journey of chronic colitis, IBS, cognitive decline, autoimmune disease, osteoporosis, arthritis, or cancer. All are gut-mediated, inflammatory conditions.
To the extent that health is an art, nowhere are your powers of expression more potent than in cultivating a healthy microbiome. Feeding and sustaining your colonocytes with smart dietary choices is an essential practice of self-care. The rewards may be subtle, such as a clear head in the morning or better energy throughout the day – or more dramatic, such as faster recovery from injuries, fewer infections, improved biomarkers, weight loss, and most of all, freedom from chronic disease. Give it time, and be patient. Like all artistic creation, the process is inseparable from the result. You are both the artist and the art – a living work in progress. Your inner garden is your individual creation. Make it beautiful.
To your good health –
Yael Bernhard
Certified Integrative Health & Nutrition Coach
Yael Bernhard is a writer, illustrator, book designer and fine art painter with a lifelong passion for nutrition and herbal medicine. She was certified by Duke University as an Integrative Health Coach in 2021 and by Cornell University in Nutrition & Healthy Living in 2022. For information about private health coaching or nutrition programs for schools, please respond directly to this newsletter, or email dyaelbernhard@protonmail.com. Visit her online gallery of illustration, fine art, and children’s books here.
Information in this newsletter is provided for educational – and inspirational – purposes only.
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https://pmc.ncbi.nlm.nih.gov/articles/PMC12647082/
https://pmc.ncbi.nlm.nih.gov/articles/PMC11242198/
https://mailchi.mp/3f3d328d2093/gutlove-weekly-14176878
https://www.sciencedirect.com/science/article/pii/S1756464625002129
https://www.mdpi.com/2304-8158/15/9/1539
Akkermansia muciniphila must be cultivated anaerobically. To my knowledge the only reputable company producing it is Pendulum. Beware of knock-offs!