PCR pathogen panel
No pathogen flagged.
Pathogen load in this sample is 0.95% of the ecosystem, inside the reference range. A panel would report nothing here, which is correct: it only asks whether named pathogens are present.
Why GutID is different
Named pathogens in their full community.
Long-read sequencing covers the full 16S gene, the ITS and the start of 23S in one ~2,500-base read, so each bacterium and its abundance appear in the Target Plot. Below: one de-identified GutID result, and what qPCR, 16S and shotgun would each have reported.
Modeled for each method
One result, read four ways.
16S rRNA · genus
Stops at genus.
Three genera hold two-thirds of this ecosystem, and 16S cannot tell you which species they contain.
Shotgun · species
Species when the database has a match.
Sharper, but still read in short fragments. What the reference cannot name stays folded into the genus above it.
Titan-1 · species + novel
Every bacterium and its share.
35.7% of this ecosystem has no assigned species name, including the second- and third-largest organisms. Long-read still separates and quantifies them.
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What qPCR does well
The right test when you know what you are looking for.
PCR and qPCR stool testing are excellent at the question they were built for: is this specific organism present? For that job they are fast and sensitive. What a panel cannot tell you is how much of the community that organism holds, or what holds the rest.
Why context matters
Gut organisms depend on one another.
Hundreds of organisms compete, cooperate, exchange metabolites and influence one another. Knowing that one bacterium is high or low without the ecosystem around it can leave out the context that changes the interpretation.
“The behavior of any given species results from the integration of its interactions with all other community members and the environment.”Coyte KZ, Rakoff-Nahoum S. Current Biology, 2019
“Cross-feeding … has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation.”Culp EJ, Goodman AL. Cell Host & Microbe, 2023
What a panel would report
A pathogen panel would likely read negative. E. coli was at 16× its reference limit.
What a pathogen panel would report
Pathogenic E. coli targets
Likely not detected
A panel looks for pathogenic E. coli genes, not for how much E. coli the community holds.
GutID ecosystem view
E. coli (all strains), as a share of the ecosystem
5.05%
Upper reference limit 0.31% · 16× the reference limit
Bacteroides uniformis alone holds 62.4% of the ecosystem.
Figures in this section come from another real GutID result, de-identified and published with permission, separate from the result in the four lenses above.
The four methods, side by side
Each method answers a different question.
The differences follow from what each method physically reads off the DNA.
| qPCR | 16S-only | Shotgun metagenomics | Titan-1 | |
|---|---|---|---|---|
| What is read | A fixed panel of chosen targets | One short variable stretch of the 16S gene | Everything present, in short fragments | The full 16S gene, the ITS and the start of 23S, in one ~2,500-base read |
| Typical resolution | Only the organisms on the panel | Genus, sometimes species | Genus to species; strain-level calls need deep sequencing | Species, from strain-level data |
| Names specific pathogens? | Yes, within the list it carries | Rarely | Where the database holds the organism | Yes, by name and quantity, against a reference range |
| Unfamiliar organisms | Not detected; absent from the panel | Often unresolved or mis-assigned | Depends on the reference database | Separated and quantified even when no species name exists |
| The question it answers | Is this organism present, and how much? | Which genera, in what proportions? | Which species, carrying which genes? | What is happening in this ecosystem? |
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Questions practitioners ask
qPCR, 16S, shotgun and long-read.
What is the difference between qPCR and sequencing in a stool test?
qPCR looks for organisms you have already named: each target on the panel is amplified and reported as present or absent, usually with a quantity. Sequencing reads the DNA that is in the sample and works out what it came from.
What does long-read add that shotgun does not?
Read length. Shotgun reads DNA in short fragments and matches them to a reference. A ~2,500-base read crosses the full 16S gene, the ITS and the start of 23S in one piece, which carries enough signal to separate close relatives and place organisms with no exact database entry.
Does GutID replace a targeted pathogen panel?
No. When you suspect a specific infection, a targeted panel is the right test. GutID adds what a panel does not report: each bacterium’s share of the whole community, against a reference range.
See what else is in the sample.
Open a clinician account to order your first GutID report, or book a call to talk it through.
