Shotgun Metagenomic Sequencing

In one line: Shotgun metagenomic sequencing looks at all the DNA in a sample at once to find which microbes are there and what jobs they might do.

What is it?

It is a lab method that reads millions of small DNA pieces from a sample such as stool, saliva, soil or water. Because it checks all DNA, it can detect bacteria, viruses, fungi and other microbes. It also shows the genes they carry, which hints at useful functions like fibre breakdown or vitamin production.

How does it work?

A small sample is collected and all DNA is extracted.

The DNA is cut into tiny fragments and fed into a sequencing machine.

Computers compare the fragments with trusted reference databases.

The output is a profile of organisms present and the functions their genes suggest.

Where does shotgun sequencing fit in?

Shotgun sequencing is the general technique of breaking DNA into many random pieces and reading them. Shotgun metagenomic sequencing applies this same idea to mixed samples that contain many species at once, for example a gut microbiome sample. So shotgun sequencing is the underlying approach, and metagenomics is the focus on whole communities.

What does it measure?

• Who is there across bacteria, viruses, archaea and fungi, often down to species and sometimes strain.
• What they can do by mapping genes to pathways and enzymes.
• Antimicrobial resistance genes that may signal potential resistance risks.

Why it matters for gut health

Your gut hosts a busy community of microbes that help digest food and support the gut lining. By reading all the DNA, this method can spot helpful functions such as short chain fatty acid production and can highlight patterns that suggest imbalance. It offers a broader picture than tests that only look at one marker or one microbe group.

Shotgun metagenomics vs 16S rRNA sequencing

How do the two main methods of gut health testing compare? We've summarised the key details of 16S rRNA sequencing and Shotgun metagenomics below.

	Shotgun metagenomics	16S rRNA sequencing
Targets	All DNA from many microbes	Bacterial 16S rRNA gene only
Taxonomic detail	Species, sometimes strain	Mainly genus level
Functional insight	Yes, genes and pathways	No direct functional readout
Cost and data size	Higher cost, larger datasets	Lower cost, smaller datasets

Strengths

• Broad view across bacteria, viruses, archaea and fungi.
• Links microbes to likely functions that matter for health.
• Finer detail, often to species or strain level.

Limitations

• More expensive and data heavy than simpler methods.
• Finds genes, which does not prove those genes are active.
• Relies on the quality and coverage of reference databases.

When is it used?

• Research into the gut microbiome and diet links.
• Public health checks for outbreaks and resistance genes.
• Environmental testing of soil and water quality.

How to read a typical report

1. Community makeup

Look for the main species and their share. Diversity often links with resilience.

2. Functional pathways

Check pathways for fibre breakdown, vitamin synthesis and short chain fatty acid production. These support gut lining and energy balance.

3. Cautions and context

Potential pathogens or resistance genes may be listed. These are signals for context and not a diagnosis on their own.

Simple example

If a report shows genes for butyrate production, it suggests the community can make butyrate, a short chain fatty acid that feeds cells in the colon. If these genes are low, eating more fibre rich foods may help encourage butyrate producers.

Common terms explained

Metagenome

All the DNA from all organisms in a sample.

Reads

Short DNA sequences produced by the sequencer.

Assembly

Piecing reads together into longer stretches to study genes or genomes.

Annotation

Labelling DNA with likely organisms and functions using databases.

Safety, privacy and ethics

Microbiome data is personal. Any test provider should explain how your sample and data are stored, who can access them and how long they are kept. In the UK, health data follows strict privacy rules. Speak to a qualified professional if you have symptoms or medical concerns.

FAQs

Is this a medical diagnosis?

No. It provides information. Only a clinician can diagnose a condition.

Can diet change my results?

Yes. Diet shapes the microbiome. Fibre rich foods such as whole grains, beans, nuts, fruit and veg often support a diverse gut bacteria community.

How long do results take?

Timings vary by provider. Ask about turnaround, method and data handling before you test.

At Vivere, your gut test results are typically ready within 4 weeks after we receive your sample. Find out more about how the process works.

Related topics

• Shotgun sequencing
• 16S rRNA sequencing
• Short chain fatty acids
• Prebiotics and probiotics
• Antimicrobial resistance

Nutritionist's Corner: Final Thoughts

"Shotgun metagenomic sequencing offers a fuller view of the gut by showing both the mix of microbes and the helpful jobs they may do. Use results as a guide alongside simple habits that support gut health, including plenty of fibre and a wide range of plant foods. If you have symptoms or a medical condition, seek advice from a qualified clinician before making changes."

Yusra Serdaroglu Aydin, MSc RD