Gut microbiome test: shotgun metagenomics or 16S?

Two main sequencing approaches are used to analyse the gut microbiome: targeted 16S gene sequencing and shotgun metagenomics. 16S sequencing is primarily used to describe the main bacterial groups present. Shotgun metagenomics examines a much broader range of microbial DNA and can provide more detailed taxonomic and functional information. The right choice therefore depends on the question being asked, the level of detail required and how the results will be interpreted.

Key point: a gut microbiome test describes a sample at a specific point in time. On its own, it cannot diagnose a disease, explain the cause of symptoms or replace a medical consultation.

16S or shotgun metagenomics: what is the difference?

Criterion	16S sequencing	Shotgun metagenomics
Principle	Targets a region of the 16S gene found in bacteria.	Sequences a broader range of DNA fragments present in the sample.
Level of detail	Generally identifies bacteria at genus level and sometimes at species level.	Can provide finer resolution, often down to species and sometimes strain level, depending on the available data.
Functional potential	Mainly inferred from the bacterial groups detected.	Can directly examine the genes detected and their potential functions.
Cost and data volume	Uses less data and is generally less expensive.	More expensive and more demanding in terms of bioinformatic analysis.
Relevant use	A broad overview of bacterial composition.	A more detailed analysis of composition and functional potential.

A comparative study published in Scientific Reports found that the two methods can produce different taxonomic profiles and that shotgun metagenomics generally provides more information at species level. This does not mean that 16S sequencing is unsuitable: each method serves different objectives, constraints and budgets.

What does a gut microbiome test actually measure?

A gut microbiome test analyses microbial DNA found in a stool sample. It provides a snapshot of the microbial composition at the time of sampling. Depending on the method and laboratory, the report may describe diversity, the species or bacterial groups detected, their relative abundance and certain potential functions associated with the genes observed.

The result should always be interpreted with caution. The gut microbiome varies with factors including diet, medication, age, lifestyle and the timing of the sample. Two tests performed at different times may therefore produce different results.

What a gut microbiome test cannot tell you

• It does not provide a medical diagnosis.
• On its own, it cannot determine the cause of pain, bloating, constipation or diarrhoea.
• It does not replace a clinical examination or tests prescribed by a healthcare professional.
• It cannot predict with certainty whether a disease will develop.
• It does not justify stopping treatment or making a major dietary change without professional advice.

If you have persistent symptoms, blood in your stool, unexplained weight loss, fever or severe pain, consult a doctor. A consumer gut microbiome test is not appropriate for a situation that requires a diagnosis.

Why Nahibu uses shotgun metagenomics

Nahibu chose shotgun metagenomics to obtain a detailed description of the microbial DNA detected in the sample. This method can examine microbiome composition at a finer resolution than 16S sequencing and explore the functional potential suggested by the genes observed.

The Nahibu report includes diversity indicators, identified species and information about functional potential. These elements describe the microbiome at the time of sampling; they do not constitute a diagnosis or a personalised prescription.

What is included in the Nahibu gut microbiome test?

• An at-home sample collection kit.
• The equipment and instructions needed to collect the sample.
• Delivery of the sample to the laboratory according to the supplied protocol.
• Analysis using shotgun metagenomic sequencing.
• A scientific report available online.
• Delivery of the kit and return of the sample included in France.

Price: €199. The stated turnaround time is 4 to 8 weeks after the laboratory receives the sample. An optional consultation with a dietitian-nutritionist may be offered separately to help you understand the report.

How should you choose a gut microbiome test?

Before ordering, check the sequencing method, the level of detail in the report, the limits of interpretation, the laboratory performing the analysis, the turnaround time, the total price and the support available. A responsible provider should clearly explain what the test measures and what conclusions it cannot support.

Also ask to see a sample report. This will help you assess whether the results are understandable, whether the indicators are explained and whether the scientific limitations are presented transparently.

Gut microbiome test FAQ

What is the best gut microbiome test? There is no single best test for every purpose. For a detailed analysis of composition and functional potential, shotgun metagenomics generally provides more information than 16S sequencing. Sample quality, bioinformatic analysis and interpretation are also important.

What is the difference between 16S sequencing and shotgun metagenomics? 16S sequencing targets a specific bacterial gene and mainly provides a broad taxonomic overview. Shotgun metagenomics analyses a wider range of DNA and can provide finer taxonomic and functional resolution.

Can a gut microbiome test diagnose a disease? No. It describes characteristics of the sample analysed, but on its own it cannot diagnose a disease, explain symptoms or replace a medical consultation.

How much does the Nahibu test cost? The Nahibu gut microbiome analysis kit costs €199, including delivery of the kit and return of the sample within France.

How long does it take to receive the results? The stated turnaround time is 4 to 8 weeks after the laboratory receives the sample. This does not include the time needed to receive the kit and return the sample.

Should I stop taking medication before collecting the sample? Never stop treatment without medical advice. Some medicines, antibiotics and supplements may affect the microbiome; follow the kit instructions and ask a healthcare professional for advice if necessary.

Scientific sources

• Durazzi F. et al. Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota. Scientific Reports, 2021.
• Ranjan R. et al. Metagenomics: a path to understanding the gut microbiome.

Informational article updated in 2026. Knowledge of the gut microbiome is evolving rapidly; test results should be interpreted cautiously and in context.