Diagnostic guide
Shotgun Metagenomic Sequencing
Species-level stool microbiome sequencing
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Evidence status: emerging or disputed. A 2025 international consensus found too little evidence for routine clinical use and discouraged self-ordered tests. Ask a licensed clinician how a result would change your care.
Cost
From $252
Turnaround
4 to 6 weeks
Ordering path
Thorne (Onegevity)
Results flow
Upload + interpret in Gabriel
Local access
Find the right local path.
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What this test reports
What this test reports
Shotgun metagenomic sequencing analyzes all the DNA in your stool sample, not just bacteria but fungi, viruses, archaea, and parasites, providing species-level identification and functional pathway analysis of your gut microbiome.
Unlike 16S rRNA sequencing (used by most consumer microbiome tests), shotgun sequencing identifies organisms to the species and strain level and shows which genes they carry, such as genes for making butyrate or LPS. Genes show potential, not what the microbes are doing on a given day.
A 2025 international expert consensus in The Lancet Gastroenterology & Hepatology found insufficient evidence to recommend routine microbiome testing in clinical practice. It discouraged ordering a test yourself without a clinician's recommendation, found no validated 'dysbiosis' score, and discouraged inferring the microbiome's metabolism from which species are present. The test can still be interesting, and tracking it over time may help; what a single result means for your health is not yet clear.
People usually reach for this kind of diagnostic when they want a clearer read on complete microbiome census (bacteria, fungi, viruses, archaea, parasites), species and strain-level identification, functional pathway analysis (what your microbiome is producing), especially when symptoms or prior testing still leave blind spots.
Once results are back, you can upload them into Gabriel to connect the findings to symptoms, protocols, and next-step testing instead of leaving them as a static report.
Commonly relevant for: Gut Issues Ibs Sibo Leaky Gut, Autoimmune Disorders, Brain Health Neurodegeneration.
Gabriel difference
Why this becomes more useful inside Gabriel
Most microbiome tests give you a snapshot of bacterial groups. Shotgun sequencing goes further: which species and strains you have and the genes they carry. Some integrative practitioners use it to track how diet and other changes shift the gut over time. The 2025 consensus suggests a licensed clinician order the test and decide any change in care. Upload your results and Gabriel explains them in plain words.
Gabriel interprets results through a functional, root-cause lens: optimal ranges, pattern recognition across multiple diagnostics, and what the findings actually mean for action rather than just classification.
That means this test can feed directly into protocols, practitioner matching, food strategy, and follow-up testing instead of ending as a one-off PDF or lab portal result.
What to expect
What to expect from ordering to results
01
Order
Order directly through Thorne (Onegevity) or ask Gabriel whether there is a better path first.
02
Complete
Collect a stool sample at home using the provided kit. Ship it in the prepaid envelope.
03
Interpret
Upload the results to Gabriel for pattern recognition, protocol suggestions, and next-step guidance.
Frequently asked questions
Questions people usually ask before ordering
GI-MAP uses targeted PCR to look for specific known pathogens. Microbiome sequencing (16S rRNA or shotgun metagenomics) sequences ALL the bacterial DNA in your sample, revealing the full diversity and composition of your gut microbiome, including species that targeted tests would miss.
You'll see which microbes are present, your microbial diversity and, with shotgun sequencing, the genes they carry (like genes for butyrate production or bile acid metabolism). A 2025 international expert consensus found too little evidence to use these results routinely in care, no validated 'dysbiosis' score, and advised against inferring metabolism from which species are present.
Popular options include Viome (metatranscriptomics, which measures microbial RNA), Thorne/OneGevity, and BiomeSight. Each uses different sequencing methods with varying depth. The 2025 consensus discourages ordering a test without a clinician's recommendation, so ask a licensed clinician first how a result would change your care.
A baseline test followed by retesting 3-6 months after dietary or supplement interventions. Your microbiome can shift meaningfully in weeks, but sustainable changes take months to establish.
Consumer kits range from $100-400 depending on sequencing depth. Viome's full panel is around $200-300. Clinical-grade sequencing through a practitioner can cost $400-600 with detailed interpretation.
Not sure which test belongs in your workup?
Tell Gabriel your symptoms, goals, and what you have already tried. You will get a more useful answer than a generic test catalog can give you.