Metagenomics and biochemistry: what each analysis reveals

If you want to understand what each test contributes, the difference is this: metagenomics describes the genetic material of the microorganisms present, while biochemistry studies molecules and metabolites related to their activity. These are complementary approaches, not substitutes for clinical assessment.

In summary:

• Metagenomics studies the genetic material present in a sample and can provide guidance on which microorganisms it contains.
• Functional biochemistry analyses molecules or metabolites associated with biological activity, such as short-chain fatty acids.
• Combining composition and function can offer a more complete view than interpreting either approach in isolation.
• Results should be interpreted alongside symptoms, medical history and the judgement of a healthcare professional.

This comparison is particularly useful when assessing an integrated microbiome, function and AI profile: it relates which microorganisms are detected to which biological activity may be observed, without treating that association as a confirmed cause.

What is the difference between metagenomics and biochemistry?

Metagenomics analyses the genetic material recovered from a sample to characterise the microorganisms and detectable genes, whereas biochemistry measures molecules present in that sample, including metabolites, which reflect biological processes. For this reason, one mainly describes composition, while the other provides information related to activity or function.

In practical terms:

• Metagenomics: mainly answers which microorganisms and genetic capabilities are detected.
• Functional biochemistry: studies compounds produced, transformed or accumulated in the environment being analysed.
• Combined interpretation: makes it possible to compare the observed composition with the molecules associated with its activity, without assuming that one automatically implies the other.

Both results depend on the type of sample, its preservation and the method used. In addition, detecting a microorganism or metabolite does not, by itself, demonstrate that it is responsible for a symptom. For further information on the underlying principles, see the microbiota blog.

What information does studying metagenomics alone provide?

Metagenomics can provide guidance on which microorganisms and microbial genes are detected in a sample, but it cannot, on its own, establish that they are active, that they are the cause of a symptom or that a disease is present: these findings must be assessed alongside the clinical history and other tests.

The analysis can help describe the microbial composition and raise questions about genes associated with specific biological capabilities. However, detecting a gene does not demonstrate that it is being expressed or that its product is affecting the body.

In an intestinal sample, for example, it is advisable to interpret the result alongside diet, medication, medical history and the reason for consultation. Sample collection and storage, the analytical method and the databases used also influence the findings. To put these results into context, the intestinal microbiota analysis can be reviewed, always as support for assessment by a healthcare professional.

What does functional biochemistry add to microbiota analysis?

Functional biochemistry provides information about the compounds that microorganisms produce or transform in the environment being studied, such as metabolites, and can complement the composition described by metagenomics. Its interpretation depends on the type of sample, how it was collected, the analytical method and each person’s clinical context.

A metabolite is a molecule generated, modified or used during biological processes. In microbiota studies, compounds associated with microbial activity may be analysed, such as short-chain fatty acids, but detecting them alone does not identify which microorganism produced them or necessarily explain a symptom.

Therefore, measuring metabolites can help assess the function observed, while metagenomics provides information about detectable microorganisms and genes. The interpretation should take into account diet, medication, intestinal transit and sample conditions. Functional short-chain fatty acid metabolomics represents this approach without replacing clinical assessment.

When does it make sense to integrate metagenomics and biochemistry?

Integrating both approaches may make sense when it is necessary to relate the microorganisms or genes detected to the compounds present in the sample, in order to develop a more complete functional hypothesis. Even so, the result does not constitute a diagnosis in itself and should be assessed alongside the clinical history and other tests.

This combination may be useful when the microbial composition does not seem sufficient to explain the activity observed, or when it is relevant to check whether the genetic findings are consistent with specific metabolites. The interpretation should take into account the sample type, its collection and storage, as well as diet, medication and symptoms.

Not all metagenomic analyses address the same question: a microbiota study should not be confused with a blood metagenomic analysis, which is intended for a different clinical context. Therefore, the value of an integrated profile depends on the specific clinical question and the healthcare professional’s judgement.

How are the results of both analyses interpreted together?

The combined interpretation should compare the microbial composition and the metabolites detected with the symptoms, medication, diet, medical history and other tests, because a correlation between a microorganism and a compound does not, on its own, confirm a causal relationship or necessarily explain a person’s clinical picture.

Before assessing the result, it is advisable to review the type of sample, how it was collected and stored, the analytical method used and whether the findings are consistent with one another. These issues can be discussed with a healthcare professional through the access available to healthcare professionals.

It is also useful to ask:

• Which findings are documented and which are only hypotheses?
• Does the sample represent the clinical environment being studied?
• Could medication or diet have influenced the metabolites?
• Which additional tests could help put the result into context?

An integrated microbiota profile can help guide a hypothesis, but it does not replace clinical assessment or allow symptoms to be attributed to a single microorganism or metabolite without further evidence.

Frequently asked questions

Can metagenomics determine whether a bacterium is causing symptoms?

No. Detecting a bacterium through metagenomics does not show that it is the cause of the symptoms. The result may provide information about its presence and suggest hypotheses, but it must be interpreted alongside the clinical history, physical examination, medication, diet and other tests. Establishing a causal relationship requires professional assessment and cannot be based solely on the microbial composition.

What types of metabolites can be studied in the microbiota?

Different microbial metabolites can be studied, including short-chain fatty acids, as well as other compounds depending on the sample and the analytical method used. Their detection provides information about the chemical environment and biological activity, but does not, on its own, identify which microorganism produced each compound or confirm a specific disease or mechanism.

Is it better to analyse the composition or the function of the microbiota?

There is no universally better option: composition and function answer different questions. The former provides information about the microorganisms or genes detected, while the latter provides information about the molecules and metabolites present. The choice depends on the aim of the study, the type of sample, the patient’s history and the clinical question that a healthcare professional needs to assess.

Can a microbiota test replace a medical assessment?

No. A microbiota test does not replace a medical assessment and should not be interpreted in isolation. Its results may provide complementary information, but symptoms and analytical findings require clinical context. The healthcare professional must decide whether further tests are appropriate, whether to establish a diagnostic orientation or whether to modify the patient’s follow-up.

What should a professional review before interpreting an integrated profile?

Before interpreting an integrated profile, it is advisable to review the type and quality of the sample, how it was collected and stored, the analytical method and which microorganisms, genes or metabolites were measured. Symptoms, medication, diet, medical history and other tests should also be taken into account. An association between composition and function does not, on its own, confirm a clinical cause.

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