Microbiome NewsA microbiome test takes a stool sample, extracts microbial DNA and reports which organisms — and sometimes which functions — are present. The gap between that one-line description and a clinically actionable result is where most of the confusion lives.
16S rRNA vs shotgun metagenomics
Two dominant methods, with very different resolution. 16S rRNA sequencing reads a single marker gene shared by bacteria; it is cheap and robust but typically resolves organisms only to the genus level and cannot read functional genes. Shotgun metagenomics sequences all the DNA in the sample, enabling species- and strain-level resolution and a readout of functional potential — at higher cost and computational complexity. Method choice constrains what any report can legitimately claim — a distinction we unpack in 16S vs shotgun: what your test actually reads.
Why two tests disagree
Every step — collection, preservation, DNA extraction, sequencing, and the reference database used to assign names — introduces variation. A 2026 NIST study found that variability between direct-to-consumer providers analysing standardized material was on the same order as the biological variability between different people. In other words, the method can contribute as much to your result as your biology does.
The pie chart is the easy part. The method that produced it — and the reference database behind it — determines whether it means anything.
What a result can and can’t do
A well-run test can describe the relative abundance of taxa and, with shotgun data, functional potential. What it generally cannot yet do is diagnose disease or prescribe a specific supplement with validated benefit for an individual. Read consumer reports as a snapshot of composition, not a clinical verdict. For the reproducibility evidence in detail, see our report on direct-to-consumer test reproducibility.
Frequently asked
Are at-home gut microbiome tests accurate?
They reliably detect DNA, but reproducibility across providers is a documented problem. A 2026 NIST study found that differences between providers analysing the same standardized sample rivaled the real biological differences between people. Treat results as approximate snapshots, not clinical diagnoses.
What does a microbiome test tell you?
It reports the relative abundance of the microbes in your sample, and — with shotgun sequencing — their functional gene potential. It generally cannot diagnose disease or validate a specific supplement recommendation for you as an individual.
What is the difference between 16S and shotgun sequencing?
16S rRNA sequencing reads one marker gene; it is inexpensive but usually resolves only to genus and reads no functional genes. Shotgun metagenomics sequences all DNA present, giving species/strain resolution and functional information, at higher cost.