Short-Chain Fatty Acids: What They Are and How Fiber Produces Them

Most of what fiber does for your health, it does by feeding bacteria. And those bacteria’s most important output isn’t just more bacteria. It’s short-chain fatty acids.

SCFAs are the molecular layer between eating fiber and the downstream health effects that research consistently associates with high-fiber diets. They’re also the reason that eating fiber from varied sources matters more than simply eating large amounts of one type.

What Short-Chain Fatty Acids Are

Fatty acids are molecules with a carboxylic acid group attached to a carbon chain. Short-chain fatty acids have chains of 1-6 carbons, making them water-soluble and fast-acting compared to the longer-chain fatty acids found in dietary fat. The three that matter most in human gut health are:

Acetate (2 carbons) is the most abundant SCFA in the colon. It’s produced broadly across many bacterial species and enters systemic circulation, where it’s taken up by peripheral tissues for energy and used as a substrate in fat synthesis.

Propionate (3 carbons) is produced primarily by Bacteroidetes species from certain fermentable fibers. It travels to the liver via the portal vein, where it participates in gluconeogenesis (making glucose) and fatty acid synthesis regulation. Research suggests propionate may help regulate cholesterol by inhibiting enzymes involved in its synthesis.

Butyrate (4 carbons) is the smallest but most locally impactful SCFA. It’s the preferred fuel for colonocytes, the cells lining the large intestine. The colon absorbs butyrate almost completely before it reaches systemic circulation, using it on-site.

Bacterial Fermentation: How It Actually Happens

Your small intestine lacks the enzymes to break down most dietary fiber. Fiber reaches the large intestine largely intact, and that’s the point. Trillions of bacteria in the colon have evolved specifically to do what your digestive system can’t: ferment these complex carbohydrates.

Fermentation is anaerobic (without oxygen). Different bacterial species specialize in different fiber substrates and produce different SCFA ratios as a result. Roseburia intestinalis and Faecalibacterium prausnitzii are among the major butyrate producers, both working on resistant starch and certain insoluble fibers. Bacteroides and Prevotella species are major propionate producers from pectin and arabinoxylan. Bifidobacterium species are primary acetate and lactate producers from inulin and FOS (Koh et al., 2016, Cell).

The ratio of SCFAs produced depends directly on which bacteria are present and which substrates are available. A microbiome that lacks butyrate-producing species will produce less butyrate even if resistant starch intake is high.

What Butyrate Does in the Colon

Butyrate’s role as colonocyte fuel is not optional. The colonic epithelium depends heavily on butyrate for energy, more than on glucose or any other substrate. Studies estimate that butyrate provides 60-70% of the energy needs of colonocytes (Topping and Clifton, 2001, Physiological Reviews).

When butyrate supply drops (due to low fiber intake or antibiotic-disrupted microbiome), colonocytes can shift to glutamine and glucose, but at a cost. The cells don’t function as well. Gut barrier integrity can suffer.

Butyrate also acts as a histone deacetylase (HDAC) inhibitor, meaning it modulates gene expression in colonocytes in ways that reduce inflammation, promote cell differentiation, and suppress abnormal cell proliferation. This is the mechanistic basis for research interest in butyrate and colorectal cancer risk (Canani et al., 2011, World Journal of Gastroenterology).

The anti-inflammatory effects extend beyond the colon. Butyrate activates GPR109A receptors on colonocytes and immune cells, suppressing NF-kB signaling (a major inflammatory pathway) and promoting regulatory T cell differentiation, which dampens excessive immune responses.

Gut Barrier Function

The gut epithelium is a single cell layer separating the contents of your intestine from your bloodstream. It’s not a solid wall. It’s a controlled gate, with tight junctions between cells that regulate what passes through.

Butyrate supports the expression of tight junction proteins including claudin-1 and occludin, helping maintain barrier integrity. When barrier function deteriorates (sometimes called “leaky gut” in popular writing, “intestinal permeability” in the literature), bacterial components like lipopolysaccharide (LPS) can cross into circulation and trigger immune activation.

The connection between adequate butyrate, gut barrier integrity, and systemic inflammation is one of the stronger mechanistic arguments for high-fiber diets affecting health beyond simple gut health.

Which Fibers Produce Which SCFAs

Not all fiber produces the same SCFA profile. Resistant starch, particularly the type in cooked and cooled potatoes and legumes, is the most reliable substrate for butyrate production. Inulin and fructooligosaccharides (FOS) from chicory, onion, and garlic feed primarily Bifidobacterium, producing more acetate.

Pectin from fruits and arabinoxylan from cereal grains feed Bacteroides species, favoring propionate. Beta-glucan from oats and barley produces a mixed SCFA profile.

Eating a wide variety of plant foods provides a range of fiber types that collectively support diverse bacterial communities. More diversity in fiber intake is more important than maximizing any single type. As the gut microbiome basics article covers, microbiome diversity is strongly linked to metabolic health.

This article is for educational purposes only. It’s not medical advice. Talk to your doctor or a registered dietitian before making significant changes to your diet.