If you have looked at microbiome testing options, you have likely encountered products using 16S rRNA sequencing or whole-genome shotgun sequencing — DNA-based methods that produce charts showing which bacterial species are present in your gut, usually compared against a reference population. These tests have genuine scientific value. They have also been commercially oversimplified to the point where many people have spent significant money on them and found the results difficult to act on.
The core limitation is that DNA tells you who is present. RNA tells you what they are doing. For health decisions, the second question is usually the more important one.
What DNA Sequencing Can and Cannot Tell You
16S rRNA sequencing — the most commonly used consumer microbiome testing method — works by identifying a specific genetic marker that all bacteria carry. By comparing sequences against reference databases, the test can enumerate which bacterial genera and species are present in your sample and in what approximate proportions. This is meaningful baseline information for research purposes and provides a general picture of microbiome diversity.
The limitation is fundamental. A bacterium can be present in your gut in significant numbers and producing nothing of clinical consequence — lying metabolically dormant, or constrained by environmental conditions that prevent gene expression. Conversely, a species present in small numbers can be highly active, expressing virulence genes, producing large quantities of inflammatory compounds, or synthesising beneficial metabolites that affect your mood, metabolism, and immune function. DNA sequencing cannot distinguish between these states. The bacteria appear identical on a population census regardless of what they are actually doing.
Research comparing DNA-based and RNA-based microbiome assessments found significant discordance between species detected by each method. Functional activity — what bacteria are actually expressing — is a poor predictor of simple species abundance, confirming that presence does not equal activity in the gut ecosystem.
How RNA Metatranscriptomics Works
RNA (ribonucleic acid) is the intermediate molecule between genetic blueprint and biological action. When a cell — whether bacterial or human — expresses a gene, it first transcribes that gene's DNA into RNA. The RNA then serves as the template for producing the proteins, enzymes, and compounds that actually affect biology. Measuring RNA reveals which genes are switched on right now, in this sample, at this moment.
Metatranscriptomics applies this principle to the entire microbial community simultaneously. Rather than sequencing which organisms are present, it sequences all of the RNA being actively produced — capturing the functional activity of the whole ecosystem. Viome's platform performs metatranscriptomics on gut (and oral) samples, generating a map of active metabolic pathways rather than a species inventory.
A DNA test shows you who is employed in the factory. An RNA test shows you who is on the production floor, what they are making, and at what rate. For health decisions, you need the second report.
This distinction becomes practically important when interpreting microbiome results. Two people can have similar bacterial species compositions — similar DNA profiles — but completely different active gene expression profiles. Their functional microbiome signatures, and therefore their health implications, may be very different. RNA-based analysis captures this; DNA analysis does not.
Why This Matters for Gut Type Confirmation
The four Gut Types are distinguished not primarily by which species are present, but by the functional outputs of the microbial community — which metabolic pathways are operating, which compounds are being produced, and at what levels. Two people with similar bacterial compositions may have different functional signatures, and therefore different type classifications, because different genes are being expressed from the same species pool.
This is why the GutType quiz — which estimates type from symptoms and dietary history — provides a useful starting point, and why RNA-based testing provides a more precise confirmation. The quiz captures the phenotypic expression of your gut type (how your body responds to food, what symptoms you experience, how your energy and mood vary). The RNA test captures the molecular mechanism directly.
It is also worth noting that Viome's metatranscriptomics platform sequences human cells alongside microbial cells in the same sample — providing cellular health markers, mitochondrial activity indicators, and immune function data that no DNA-only microbiome test produces. This broader biological picture is part of what distinguishes a clinical-grade analysis from a consumer microbiome curiosity product.
Get your estimated Gut Type in 3 minutes. Use the RNA test to confirm it with molecular precision when you're ready.
Sources & Further Reading
- Franzosa, E.A., et al. (2014). Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences, 111(22), E2329–E2338.
- Lloyd-Price, J., et al. (2019). Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature, 569, 655–662.
- Schirmer, M., et al. (2016). Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell, 167(4), 1125–1136.
- Integrative HMP (iHMP) Research Network Consortium (2019). The Integrative Human Microbiome Project. Nature, 569, 641–648.
