The Microbiome

What Is Faecal Metabolomics?

Faecal metabolomics looks at small molecules present in stool samples to help researchers understand the chemical environment within the gut. It can reveal changes associated with microbial activity, digestion and host metabolism that are not visible from microbiome composition alone.

Science explainer

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Science explainer

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Faecal metabolites and gut metabolic activity

What is faecal metabolomics?

Microbiome analysis can tell us which bacterial groups are present in a faecal sample.

But that does not automatically tell us what is happening chemically within the gut.

Faeces contain a large number of small molecules produced from several sources, including food, digestion, microbial activity and the dog's own metabolism.

Studying these molecules can help researchers ask a different kind of question:

What chemical changes are occurring within the gut environment, and how do they relate to digestion and the microbiome?

How are metabolites in stool samples analysed?

Faecal metabolomics uses analytical techniques to identify and measure small molecules present in stool samples.

Sample collection

Researchers collect faecal material under controlled conditions and store it carefully to reduce changes after sampling.

Chemical analysis

Different analytical platforms can be used, including mass spectrometry, gas chromatography and nuclear magnetic resonance spectroscopy.

Targeted analysis

Researchers may measure a defined group of compounds they already want to investigate.

Untargeted analysis

Broader approaches can detect a much wider range of molecules, allowing unexpected patterns to emerge.

The resulting data can then be compared between dogs, diets, time points or interventions.

Which compounds can faecal metabolomics measure?

Faecal metabolomic studies may examine many different groups of compounds.

Short-chain fatty acids

These include acetate, propionate and butyrate, which are produced during microbial fermentation.

Alcohols and other volatile compounds

Compounds such as ethanol and methanol may also be detected.

Nitrogen-related compounds

Microbial metabolism of proteins and amino acids can produce compounds including ammonia and other nitrogen-containing metabolites.

Bile acid derivatives

Gut microorganisms can modify bile acids, producing secondary metabolites.

Lipid-related compounds

Fats from diet and host metabolism can also contribute to the faecal metabolome.

Looking across many compounds can provide a chemical fingerprint of the gut environment at the time of sampling.

Why can metabolite profiles differ from bacterial profiles?

Faecal metabolomics is useful because biological activity can change even when the composition of the microbiome changes only modestly.

Two dogs may have microbial communities that look broadly similar but produce different metabolite profiles.

The opposite can also occur.

Microbial composition may change while some metabolic functions remain relatively stable.

This is one reason researchers increasingly combine microbiome analysis with metabolomics.

Together, these methods can help distinguish between:

who is present

and

what is happening chemically within the gut

How does faecal metabolomics help explain the gut ecosystem?

Faecal metabolomics provides another layer of information about the gut ecosystem.

It helps connect microbial composition with the compounds being produced, transformed or left behind.

This is especially relevant when studying the relationship between digestion and the microbiome.

If digestion changes the substrate reaching microbial communities, the metabolic products generated downstream may also change.

That creates a useful sequence:

Digestion → Substrate → Microbial activity → Metabolites

Faecal metabolomics therefore helps researchers investigate the functional side of the gut rather than focusing only on bacterial abundance.

For a method that identifies bacterial groups rather than metabolites, read our guide to 16S microbiome analysis.

What can a faecal metabolite result leave uncertain?

Faecal metabolomics has several important limitations.

Origin of metabolites

A compound found in faeces may come from the diet, the dog, microorganisms, or a combination of all three.

End-point measurement

Faeces represent what remains at the end of the digestive tract.

Some compounds may already have been absorbed, transformed or used earlier.

Sample handling

Storage conditions, time before freezing and laboratory methods can influence measured concentrations.

Biological variation

Metabolite profiles can vary substantially between individual dogs.

For these reasons, faecal metabolomics is most informative when combined with microbiome, dietary and physiological data rather than interpreted on its own.

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.

Waring RH, Dagi TF, Hunter JO. Innovative Approaches to Managing the Mammalian Microbiome: Evidence for the Role of Anabiomics. Journal of Modern Agriculture and Biotechnology. 2024;3:10.

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