Glossary · Nutrition and probiotics
Short-chain fatty acids
In one sentence
Short-chain fatty acids (SCFAs) are fatty acids with one to six carbon atoms produced by colonic bacteria when they ferment fibre and other non-digestible carbohydrates. The main ones are acetate, propionate and butyrate.
Also known as: SCFA · SCFAs · short-chain fatty acid · short chain fatty acids
What are short-chain fatty acids?
Short-chain fatty acids are the main end products of fermentation by the microbiota of the large intestine. When dietary fibre and resistant starch reach the colon undigested, bacteria convert them into SCFAs as well as gases such as hydrogen and carbon dioxide.
The three dominant SCFAs are:
- Acetate (C2): the most abundant; much of it enters the bloodstream and reaches peripheral tissues.
- Propionate (C3): taken up largely by the liver, where it feeds into gluconeogenesis.
- Butyrate (C4): used mainly by colonic epithelial cells as fuel.
A classic autopsy study (Cummings et al., Gut, 1987) found high SCFA concentrations throughout the colon, peaking in the caecum, with levels falling from portal to peripheral blood — consistent with uptake by the gut lining and the liver. Acetate predominated in every compartment sampled.
What they do
According to the review by Mukhopadhya and Louis (Nature Reviews Microbiology, 2025), SCFAs:
- Provide energy to the colonic epithelium.
- Help keep the colonic lumen mildly acidic.
- Act as signalling molecules through receptors such as FFAR2 and FFAR3, shaping immune responses.
- Take part in glucose and lipid metabolism.
Many of these mechanisms come from cell and animal studies. In humans most data are associative, and the link between a given faecal value and a clinical outcome has not been established.
How they are measured
The reference technique is gas chromatography-mass spectrometry (GC-MS), which separates, identifies and quantifies each fatty acid. Bear in mind that faecal concentration reflects the balance between production and absorption: most SCFAs are absorbed in the colon, so the stool value is not the same as total production. Recent diet, transit time and how the sample is stored all play a part, and reference ranges differ between laboratories.
Example
A gastroenterologist sees a patient with irritable bowel syndrome who has followed a very low-fibre diet for months. The faecal profile shows acetate, propionate and butyrate below the laboratory range, with normal relative proportions. The clinician reads this as reduced fermentative activity in keeping with the diet and weighs it alongside the rest of the assessment, without treating it as a diagnosis.
Short-chain fatty acids at Xenogene
Xenogene’s functional metabolomics test uses GC-MS to quantify butyrate, propionate and acetate in stool, reporting concentrations and relative proportions. It is most informative within an integrated profile alongside gut microbiota metagenomics: composition shows who is there, while SCFAs show part of what they are doing. For more on the approach, see metabolomics. The test requires a prescription and interpretation rests with the requesting professional.
Frequently asked questions
Which foods help produce short-chain fatty acids?
SCFAs come mainly from bacterial fermentation rather than from food itself. Pulses, wholegrains, oats, fruit, vegetables and resistant starch (for instance cooked and cooled potatoes or rice) supply fermentable substrates. How much is produced depends on each person's microbiota.
Can you take SCFA supplements?
Supplements exist, mostly butyrate, but clinical evidence in humans is limited and inconsistent. Whether they make sense for a particular person is a question for a healthcare professional.
What does a low SCFA result in stool mean?
It may reflect a low-fibre diet, reduced fermentation, or changes in transit or absorption. It is not a diagnosis on its own and is interpreted alongside diet, symptoms and the microbiota profile.
Related terms
- Butyrate
Butyrate is a four-carbon short-chain fatty acid produced by certain colonic bacteria when they ferment fibre. It is the main energy source for colonocytes and contributes to the function of the intestinal barrier.
- Dietary fibre
Dietary fibre is the group of plant carbohydrates, plus lignin, that the human small intestine cannot digest or absorb. It reaches the colon, where it adds bulk to stools and is partly fermented by the gut microbiota.
- Metabolomics
Metabolomics is the large-scale study of metabolites — the small molecules produced by the activity of cells and microorganisms — in a biological sample such as blood, urine or stool. It reflects what is happening in a system at a given moment.
- Microbiota
The microbiota is the community of living microorganisms (bacteria, archaea, fungi, protozoa) that inhabits a specific site of the body, such as the gut, mouth, skin or vagina.
- Prebiotic
A prebiotic is a substrate that is selectively utilised by host microorganisms and confers a health benefit, according to the 2017 consensus definition of the International Scientific Association for Probiotics and Prebiotics (ISAPP).
Educational content for healthcare professionals and the general public. It does not replace assessment by a healthcare professional: ordering and interpreting any test is the responsibility of the requesting clinician.
Updated on