Microbiome testing has become increasingly popular, but not all gut tests are created equal. If you’ve ever wondered why results can look very different depending on the test used — or why one practitioner recommends one type over another — the answer lies in how the microbiome is analysed.

Broadly speaking, there are three main approaches to gut microbiome testing:

  • Culture-based testing

  • 16S rRNA sequencing

  • Shotgun metagenomic sequencing

Each has strengths, limitations, and appropriate use cases. Understanding the differences can help you make sense of your results — and avoid frustration or confusion.

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1. Culture-Based Stool Testing (The Traditional Method)

How it works

Culture-based tests attempt to grow bacteria from a stool sample in a laboratory. Specific media are used to encourage the growth of certain organisms, which are then identified.

What it can tell us:

  • Presence of some pathogenic bacteria or yeasts

  • Antibiotic or antimicrobial sensitivity testing (for organisms that grow)

Key limitations

  • Only organisms that grow well in lab conditions are detected

  • Antibiotic or antimicrobial sensitivity testing (for organisms that grow)

  • Provides a very narrow snapshot of the microbiome

Best used for

  • Only organisms that grow well in lab conditions are detected

  • Antibiotic or antimicrobial sensitivity testing (for organisms that grow)

  • Provides a very narrow snapshot of the microbiome

Culture tests reflect a small fraction of the gut ecosystem. They can be useful in targeted clinical situations, but they do not represent overall microbiome health.

2. 16S rRNA Sequencing (A Broad Overview)

How it works

16S testing looks for a specific genetic marker (the 16S ribosomal RNA gene) that is shared by bacteria. By analysing this gene, the test can identify bacteria present in the sample.

What it can tell us

  • Relative abundance of bacterial groups

  • Microbial diversity

  • Broad patterns such as dysbiosis or low diversity

Strengths

  • Detects both aerobic and anaerobic bacteria

  • Provides a much broader view than culture

  • Broad patterns such as dysbiosis or low diversity

Limitations

  • Usually identifies bacteria only to genus level, not species

  • Does not detect viruses, fungi, yeasts, or parasites

  • Provides limited functional insight (what the microbes are doing)

Best used for

  • General gut health screening

  • Research and population studies

  • Clients wanting a high-level overview

16S testing gives a helpful “big picture” of bacterial balance, but it lacks the depth needed for truly personalised or targeted interventions.

3. Shotgun Metagenomic Sequencing (The Most Comprehensive Option)

How it works

Shotgun sequencing analyses all genetic material in a stool sample — not just one marker gene. This allows identification of bacteria, viruses, fungi, yeasts, archaea, and sometimes parasites, as well as the genes they carry.

What it can tell us:

  • Species- and sometimes strain-level identification

  • Bacteria, viruses, fungi and yeasts

  • Functional pathways (e.g. short-chain fatty acid production, neurotransmitter metabolism, bile acid metabolism)

Limitations

  • Higher cost

  • Requires expert interpretation to avoid over-treatment or misinterpretation

Strengths

  • Most detailed and comprehensive approach

  • Links microbial composition to function

  • Allows more personalised dietary and supplement strategies

Best used for

  • Complex or long-standing gut issues

  • Recurrent symptoms where basic testing hasn’t helped

  • Clients wanting precision and personalised guidance

Shotgun sequencing provides the deepest insight into both who is in the gut and what they’re doing. When interpreted correctly, it offers the most clinically useful information.

Why Test Choice Matters

Two people can have the same symptoms and receive very different results depending on the test used. This doesn’t mean one result is “wrong” — it means the lens is different.

  • Culture tests look at a few organisms

  • 16S looks broadly at bacterial balance

  • Shotgun sequencing looks deeply at the entire ecosystem and its function

Choosing the right test depends on symptoms, history, goals, and how much detail is needed to guide treatment.

Final Thoughts

Microbiome testing is a powerful tool — but only when the right test is chosen and the results are interpreted in context. More data isn’t always better, and less data isn’t always enough.

If you’re considering microbiome testing, working with a practitioner who understands the strengths and limitations of each method ensures the results lead to clarity, not confusion — and to a plan that actually supports your gut health long-term.

Microbiome Test Comparison: At a Glance

Feature Culture-Based Testing 16S rRNA Sequencing Shotgun Metagenomic Sequencing
What’s analysed Bacteria grown in a lab Bacterial 16S rRNA gene All microbial DNA
Microbes detected Limited bacteria, some yeasts Bacteria only Bacteria, viruses, fungi, yeasts, archaea (± parasites)
Anaerobic bacteria Mostly missed Detected Fully detected
Level of identification Species (for those that grow) Mostly genus level Species and sometimes strain level
Functional insight (what microbes do) None Minimal Detailed (metabolic & inflammatory pathways)
Diversity analysis No Yes Yes
Pathogen detection Limited Moderate Broad and detailed
Antibiotic sensitivity testing Yes (for cultured organisms) No No
Clinical depth Low Moderate High
Typical cost Low Moderate Higher
Best suited for Acute infections, targeted pathogens General gut health overview Complex, chronic or unexplained gut issues
Main limitation Misses most of the microbiome Limited resolution and function Requires expert interpretation

Think of culture testing as a snapshot, 16S as a wide-angle lens, and shotgun sequencing as a high-resolution, full-ecosystem analysis.