Glossary · Markers and tests
Metabolomics
In one sentence
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.
Also known as: metabolomic · functional metabolomics · metabolome · metabolómica
What is metabolomics?
Metabolomics is one of the “omics” disciplines, alongside genomics, transcriptomics and proteomics. Its subject is the metabolome: the full set of small molecules (sugars, amino acids, organic acids, lipids, bile acids and so on) present in a sample. These compounds come from our own cells, from diet and, in the gut, from the microbiota.
Its practical appeal is that it sits at the end of the biological chain. Genes indicate capabilities; metabolites show the activity that is actually taking place. The field’s reference resource, the Human Metabolome Database (HMDB 5.0; Wishart et al., Nucleic Acids Research, 2022), lists more than 200,000 compounds detected or predicted in humans.
How it works
There are two broad approaches:
- Targeted: measures a defined set of metabolites against reference standards and gives quantitative concentrations. This is the approach used in diagnostics because it is more reproducible.
- Untargeted: tries to capture as many signals as possible to discover differences between groups. It belongs mainly to research and generates hypotheses rather than clinical results.
The main techniques are gas or liquid chromatography coupled to mass spectrometry (GC-MS, LC-MS) and nuclear magnetic resonance (NMR) spectroscopy. GC-MS is particularly suited to volatile compounds such as short-chain fatty acids.
What it adds to microbiota testing
Combined with sequencing, metabolomics moves the question from “who is there?” to “what are they doing?”. The same taxonomic profile can come with different metabolic output, and vice versa. Measuring butyrate, for example, adds a functional layer that sequencing alone cannot provide. Every metabolite measured can act as a biomarker, with the usual caveats: biological variability, dietary influence and differences between methods and laboratories.
Example
A clinician requests both a microbiota study and a faecal SCFA profile. Sequencing shows plenty of butyrate-producing bacteria, yet metabolomics finds low butyrate. The mismatch prompts a look at diet (little fermentable fibre) or transit, rather than assuming that the presence of these bacteria means they are active.
Metabolomics at Xenogene
Xenogene’s functional metabolomics is a targeted test: it uses GC-MS to quantify butyrate, propionate and acetate in stool, reporting concentrations and relative proportions. It is designed to be read alongside metagenomics in the integrated profiles. The test requires a prescription, and interpretation is the responsibility of the requesting professional.
Frequently asked questions
What is the difference between metabolomics and genomics?
Genomics studies DNA, which describes an organism's potential. Metabolomics measures metabolites, which reflect actual activity at that moment. Put simply, genomics tells you what could happen and metabolomics tells you what is happening.
What is a metabolomics test used for?
In clinical practice it is used to measure specific metabolites with established value, such as newborn screening for inborn errors of metabolism or short-chain fatty acids in stool. In research it is used to search for new biomarkers. Results always depend on clinical context.
What sample does a metabolomic study need?
It depends on the question: blood, urine, stool, saliva or tissue. For gut microbiota work, stool is used, with strict collection and storage conditions so that metabolites do not degrade.
Related terms
- Short-chain fatty acids
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.
- 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.
- Biomarker
A biomarker is a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, disease processes or responses to a therapeutic intervention. It may be a molecule, a genetic variant or an imaging finding.
- Microbiome
The microbiome is the microbial community of a habitat together with its "theatre of activity": its genes, metabolites and surrounding environmental conditions. It is broader than the microbiota.
- Shotgun metagenomics
Shotgun metagenomics sequences all the DNA in a sample in an untargeted way, without amplifying a single marker gene. It can identify bacteria, DNA viruses, fungi and parasites, often to species level, and reveal their functional and resistance genes.
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.
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