Why Sample Preservation Matters in Microbiome Testing

Some microbiome companies do not preserve their stool samples, which can seriously affect the results.

The quality of a microbiome test is determined long before sequencing begins.

Consumers often compare sequencing technologies, species detection, or AI-powered interpretation. But one of the most important factors influencing the accuracy of any microbiome test is much simpler:

Does the stool sample remain representative of the original microbiome while it is being shipped to the laboratory?

If the microbial community changes during transport, even the most sophisticated sequencing platform can only measure the altered sample, not the microbiome that was originally present.

Stool is a living biological sample

Stool contains trillions of living microorganisms that continue to grow, die, and interact after collection.

Without an effective preservation method, room-temperature storage can lead to:

· Growth of some microorganisms while others decline

· Loss of oxygen-sensitive bacteria

· DNA degradation

Because microbiome sequencing reports relative abundances, even modest growth of one organism changes the apparent abundance of every other organism in the sample.

The scientific literature consistently shows that preservation matters

Multiple independent studies have demonstrated that unpreserved stool stored at room temperature undergoes measurable changes in microbial composition.

For example, Wang and colleagues compared frozen stool with several preservation methods and with stool stored at room temperature without preservative. Samples stored without preservation diverged from frozen controls, showing reduced microbial diversity and altered microbiome composition.

Similarly, Poulsen and colleagues evaluated multiple stool collection methods using shotgun metagenomics. They reported that conventional dry swabs exhibited unpredictable overgrowth of Escherichia in at least one replicate from every participant, demonstrating that collection method alone can influence measured microbial profiles.

Byrd and colleagues reached a similar conclusion across three separate study populations, finding that the reproducibility, stability, and accuracy of microbial profiles varied substantially depending on the collection method used, with unpreserved samples generally performing worse than those stored in an effective stabilization solution.

These findings reinforce an important principle: sample preservation is not merely a logistical convenience—it is a fundamental component of analytical accuracy.

Sequencing technology cannot correct pre-analytical errors

Modern shotgun metagenomic sequencing is remarkably powerful. It can identify microorganisms at species and, in many cases, strain resolution.

However, sequencing cannot recover information that has already been lost or altered before laboratory processing.

No bioinformatics algorithm can determine whether a bacterium became abundant because it was truly abundant in the gut or because it multiplied during shipment.

This is why clinical laboratory medicine places such importance on validating the entire workflow, from collection through reporting.

Viome has published validation of its complete collection workflow

At Viome, we believe that every step of the analytical process should be scientifically validated, not just the sequencing platform.

Our published metatranscriptomic validation study describes an integrated sample-to-result workflow that includes:

· A proprietary ambient-temperature preservation solution

· Validation of sample stability during room-temperature shipping

· Reproducible RNA extraction

· Species-level taxonomic accuracy

· Quantitative microbial gene expression analysis

· Automated quality-control procedures throughout laboratory processing

In our validation studies, stool samples remained stable during ambient-temperature transport for up to 28 days, enabling reliable analysis even with routine shipping times. The platform was further validated across more than 100,000 human stool samples, demonstrating reproducibility, accuracy, and scalability for population-scale microbiome research.

Questions every consumer should ask

When evaluating any microbiome test, consider asking:

· Has the complete collection method been validated in a peer-reviewed publication?

· Does the collection tube include an effective stabilization solution?

· Has stability been demonstrated under real-world shipping conditions?

· Were results compared with immediately processed or frozen samples?

· Is the validation published and available for independent review?

These questions are just as important as the sequencing technology itself.

Accuracy begins at collection

Microbiome testing is only as reliable as the sample that reaches the laboratory.

Scientific evidence consistently shows that sample collection and preservation influence microbiome measurements. That is why Viome has invested in validating not only its sequencing technology, but the entire analytical workflow—from the moment a sample is collected until clinically meaningful results are generated.

When it comes to microbiome science, accuracy doesn't start in the sequencer, it starts with the sample.

References

Hatch A, Horne J, Toma R, et al. A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health. International Journal of Genomics. 2019;2019:1718741.

Wang Y, et al. A comparison of fecal collection methods for microbiome and metabolomics studies. Frontiers in Cellular and Infection Microbiology. 2022.

Poulsen CS, et al. Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME Communications. 2021.

Byrd DA, et al. Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations. PLoS ONE. 2019.