The Microbiome

Short-Chain Fatty Acids: What Are They and Why Do They Matter?

Short-chain fatty acids are produced when gut microorganisms ferment certain substrates. They are among the best-studied products of microbial activity and provide a useful window into the relationship between diet, digestion and the metabolic activity of the microbiome.

Science explainer

Short-Chain Fatty Acids: What Are They and Why Do They Matter?

Content type

Science explainer

Focus

Short-chain fatty acids, fermentation and microbial metabolism

The big question

Gut microorganisms do more than simply live alongside the food passing through the digestive tract.

They actively use available substrates and transform them into new compounds.

Among the best known of these compounds are short-chain fatty acids, often abbreviated to SCFAs.

These are produced during microbial fermentation of certain nutrients, particularly carbohydrates that have escaped digestion earlier in the gastrointestinal tract.

Because their production depends on both the available substrate and the microorganisms using it, SCFAs provide an interesting link between digestion and microbial activity.

So what are they, and what can they tell us about the gut environment?

How do scientists study it?

Short-chain fatty acids are small organic acids produced largely through microbial fermentation in the lower gastrointestinal tract.

The main SCFAs usually discussed are acetate, propionate and butyrate.

Different microorganisms can use different substrates and fermentation pathways, meaning the pattern of SCFAs produced can vary according to both the microbial community and the nutrients available to it.

Researchers can measure SCFAs in intestinal contents or faecal samples using analytical techniques such as gas chromatography or liquid chromatography.

These measurements are often combined with microbiome analysis and dietary information to help researchers understand how the nutritional environment and microbial community are interacting.

What can we measure?

SCFA research usually looks at several related factors.

Total SCFA concentration

The overall amount of short-chain fatty acids detected in a sample.

Individual SCFAs

Researchers may measure acetate, propionate and butyrate separately.

Substrate availability

The type and amount of fermentable material reaching the lower gastrointestinal tract can influence SCFA production.

Microbial composition

Different microbial communities may produce different fermentation patterns.

Dietary context

Changes in fibre type, carbohydrate availability and overall diet composition can alter both microbial fermentation and the resulting metabolite profile.

These measurements help researchers connect what reaches the microbiome with what the microbiome produces.

What have we learned?

One of the clearest findings from gut microbiome research is that short-chain fatty acid production depends heavily on substrate availability.

When fermentable carbohydrates reach microbial communities, certain bacteria can use them and produce SCFAs as metabolic end products.

Different substrates can favour different fermentation pathways, meaning both the quantity and relative proportions of individual SCFAs may change.

But SCFA concentrations should not be interpreted too simply.

The amount detected in faeces represents only what remains at the point of sampling.

Some SCFAs may already have been absorbed or used elsewhere in the gastrointestinal tract.

For that reason, SCFAs are best viewed as useful indicators of microbial fermentation rather than as a complete measure of everything occurring within the gut.

Why does this matter?

Short-chain fatty acids help illustrate why microbiome function matters.

A list of bacterial names tells us which microorganisms may be present.

SCFAs give us information about one aspect of what those microbial communities are doing.

They also reinforce the importance of substrate.

Microorganisms can only ferment the material available to them.

That creates another useful connection:

Digestion → Substrate reaching the lower gut → Microbial fermentation → Metabolites

This is one reason the nutritional environment around the microbiome is so important when trying to understand microbial activity.

For an example of research measuring microbial and metabolic changes, read the independent canine fibre study.

What should we keep in mind?

Short-chain fatty acids are useful markers of microbial fermentation, but they do not provide a complete picture of microbiome function.

Different microorganisms can produce the same SCFA, so the presence of a particular compound does not necessarily reveal which bacteria produced it.

Faecal concentrations also reflect the balance between production, absorption, further metabolism and excretion.

A lower faecal concentration does not automatically mean that less was produced, and a higher concentration does not automatically mean that more is beneficial.

Diet, transit time, sampling location and analytical method can all influence the result.

For that reason, SCFA measurements are most informative when interpreted alongside microbiome composition, diet and other metabolic data.

Sources and further reading

References

Further reading:

Pilla R, Suchodolski JS. The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease. Frontiers in Veterinary Science. 2020;6:498.

Wernimont SM, Radosevich J, Jackson MI, et al. The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease. Frontiers in Microbiology. 2020;11:1266.

Deng P, Swanson KS. Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges. British Journal of Nutrition. 2015;113:S6–S17.

Suchodolski JS. Diagnosis and interpretation of intestinal dysbiosis in dogs and cats. The Veterinary Journal. 2016;215:30–37.

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