5 laboratory best practices in metagenomics

The reliability of a metagenomic analysis depends on a traceable, controlled process: documenting the sample, preventing contamination, reviewing sequencing and bioinformatics, and explaining the limitations of the results.

In summary:

• The quality of a metagenomic analysis depends on reviewing each stage, from sample receipt to data analysis.
• Documenting sample traceability and preventing contamination help determine whether the results can be interpreted.
• Quality control criteria for sequencing and bioinformatics should take into account the sample type and the purpose of the analysis.
• A metagenomic report can provide guidance, but it should be interpreted alongside the clinical context and does not replace assessment by a healthcare professional.

When consulting a laboratory, it is worth asking which stages it documents and how it explains the limitations of its results.

How is the traceability of a metagenomic sample ensured?

The traceability of a metagenomic sample is documented by recording its identification and each stage from receipt through processing, together with any incidents and the applicable storage and transport conditions. These requirements depend on the type of sample and should be defined in validated instructions for that material, rather than extrapolated from other sample types.

As a review criterion, the documentation should make it possible to check that the sample identification matches the request and to establish the condition in which it was received, how it was stored and which processing stages were recorded. It is also useful to document any incidents that could affect interpretation, without assuming that all sample types require the same conditions.

Before sending a sample, ask the laboratory which collection and transport instructions apply to it and how to report an incident. You can review the analyses available from Xenogene and request information about the instructions applicable to each test. These recommendations describe what is useful to check; they do not, by themselves, confirm Xenogene’s internal procedures.

Which controls help detect contamination during the process?

Negative controls help detect signals that may come from reagents or contamination introduced during processing. Positive controls help check whether an analytical step can recover the expected material. Both should be interpreted in the context of the sample, method and objective, rather than treated as a universal setup.

To reduce the risk of contamination, preventive measures may include separating preparation and extraction areas, using clean materials, and minimising unnecessary openings and transfers. These are general recommendations, not a description of Xenogene’s protocol.

The type and number of controls should be determined by the analysis design and the steps to be assessed. When ordering a microbiome test, it is worth asking which controls are used, what they help check and how they are considered when interpreting the report. The presence of controls does not, by itself, show that a result is free from contamination: their role is to provide information for assessing the process.

How is the quality of metagenomic sequencing controlled?

Quality control for metagenomic sequencing assesses whether the data obtained are suitable for the intended analysis. It applies criteria defined according to the sample type, platform and analytical objective. There is therefore no single threshold that can be applied to every study.

When requesting an analysis, it is worth asking whether the criteria are set for the sample and the analytical question, what happens if the data do not meet them, and whether any limitations could affect the interpretation. The indicators and acceptance criteria should be supported by relevant technical documentation or validated laboratory procedures; they should not be assumed to be the same across methods.

If you are evaluating a Nanopore-based analysis, the comparison between Nanopore and culture provides context on these methods. The platform alone does not indicate whether the data are sufficient to answer a specific clinical question.

What should be documented in the bioinformatics analysis?

For a metagenomic result to be reviewed, the laboratory should document the tools and their versions, the databases consulted, the criteria used to classify sequences, and any relevant processing decisions. This information helps explain how the result was obtained, without attributing procedures to the laboratory that it has not confirmed.

When reviewing a report, ask whether it identifies these resources, when they were used, and what criteria were followed to interpret ambiguous results. The databases and their versions provide context about the references considered; filtering and classification decisions are also part of the method and are useful to know. Do not assume that Xenogene uses any specific tools, databases, or versions without documentary confirmation.

Healthcare professionals can visit the healthcare professionals’ portal to request information about the method used.

How are the limitations of a metagenomic report communicated?

A metagenomic report communicates what material was analysed and what results were obtained, but it should not present a detection as an automatic explanation for symptoms. Establishing its clinical relevance requires assessing the person’s context and is the responsibility of a healthcare professional.

When reviewing a report, it is useful to distinguish the analytical finding from its clinical interpretation and ask what it means in relation to the sample and the reason for testing. The absence of a detection should not be interpreted beyond what the analysis performed allows. Without information about the specific method and sample, it is not appropriate to attribute specific limitations or conclude what can or cannot be ruled out.

To understand the result, it may be useful to consult the healthcare professional responsible for the assessment. Sophia, Xenogene’s clinical AI can help interpret reports, but does not replace clinical judgement or healthcare assessment.

Frequently asked questions

What is the difference between metagenomics and microbiological culture?

Metagenomics analyses genetic material present in a sample, while culture looks for microorganisms that can grow under laboratory conditions. Because they use different methods, they can provide different information, and their results are not interchangeable. The appropriate technique depends on the clinical question, the sample type and the healthcare professional’s assessment.

What information should I ask the laboratory for before requesting a test?

It is useful to ask what type of sample is needed, how it should be collected and stored, what the test analyses and what limitations the report has. You can also ask what methodological information the laboratory can provide and how questions about the results are handled. The answers should relate to the specific test, not be a generic description.

Can results from two laboratories be compared directly?

You should not assume that two results are directly comparable: the sample type, method, analysis criteria and way findings are presented may differ. Before drawing conclusions, ask whether both laboratories analysed equivalent samples and used comparable procedures. Interpretation should take these differences and the clinical context into account.

Can I collect the sample at home before sending it to the laboratory?

This depends on the test and the sample type: collection, storage and shipping instructions may differ. Follow the instructions provided for the specific test, and contact the laboratory if anything is unclear before collecting the sample. Do not reuse instructions from another test, as they may not be suitable for that sample.

Ask the Xenogene team for information about the metagenomic tests available.