# OpenBiota Gut Health Test
**Raw shotgun sequencing reads in. A gut-health report you can actually read out.**
The OpenBiota software (`openbiota` on the command line) takes the paired-end
FASTQ files behind a shotgun stool metagenome and turns them — every read, no
subsampling — into the OpenBiota Gut Health Test: a gut-health index,
species-level community composition, copies-per-100-genomes capacity for 25
metabolite pathways, resemblance scores against 33 published disease-associated
microbiome patterns, a 485-target pathogen screen and an estimated microbiome
age. Page one is the whole answer in graphics; the pages behind it are the
evidence, and every number traces back to the reads that produced it.
## Two sample reports
Two complete reports from real samples ship with the project, so you can read
one before sequencing anything. The same software produced both; the two
communities sit at opposite ends of the scale.
[{ width="360" }](https://raw.githubusercontent.com/openbiota-org/openbiota-gut-health-test/main/sample-reports/EM1_AMD614_report.pdf)
Broadly disturbed. Index −1.35: an opportunist overgrown at ×110 its typical carrier, six core species missing, butyrate at the 5th percentile. Download the full report (PDF, 2.1 MB)
[{ width="360" }](https://raw.githubusercontent.com/openbiota-org/openbiota-gut-health-test/main/sample-reports/MM1_FXX745_report.pdf)
Healthy range. Index +2.00: 26 health markers to 3 disease markers, a protective gut lining at 97/100, two organisms modestly above their typical carrier. Download the full report (PDF, 1.9 MB)
Page 1 is the whole answer in graphics: the gut-health dial, what stood out,
every metabolite pathway on one shared scale, the community donut and
disease-pattern resemblance. Behind it, the same pages for each report:
Broadly disturbed: organisms that need attention · what you can do about it · estimated age · disease patterns
Healthy range: the same four pages
!!! warning "Research software. Not a medical device. Not medical advice. No warranty, no liability."
The report measures *genetic capacity* and *community resemblance*. It does
not measure metabolites and it does not diagnose disease. A match to a
disease signature is a clue for further investigation, not a diagnosis.
OpenBiota has not been reviewed or cleared by the FDA, EMA, MHRA or any
other regulator. Nothing it produces diagnoses, treats or prevents any
condition, and nothing tells you to start, stop or change a medication,
supplement, food or treatment. Where a report describes a food, compound,
supplement, botanical, probiotic, drug or procedure, it is *describing
published research*, not recommending it. The software, its reference data
and all of its output are provided **as is**, with all faults and no
warranty of any kind; you use them entirely at your own risk and on your
own judgement. Talk to a qualified clinician before acting on anything
here. Full terms:
[DISCLAIMER](https://github.com/openbiota-org/openbiota-gut-health-test/blob/main/DISCLAIMER.md)
and the *NO WARRANTY, NO MEDICAL ADVICE, NO LIABILITY* section of the
[licence](https://github.com/openbiota-org/openbiota-gut-health-test/blob/main/LICENSE).
## Where to start
- **[Quickstart](QUICKSTART.md)**
From a fresh clone to your first PDF: tools, reference data, one command.
- **[Installation](INSTALL.md)**
macOS and Linux, the two MetaPhlAn environments, verifying the install.
- **[Usage](USAGE.md)**
Every `openbiota` command and flag, caching, performance tuning.
- **[Reading the report](OUTPUT.md)**
What each section means, the seven-band scale, `results.json`.
- **[Method](METHOD.md)**
How the measurements are made and why they are made that way.
- **[Validation](VALIDATION.md)**
Sensitivity, specificity, the reference cohort, and a like-for-like
comparison against a commercial report.
- **[Organism detection](EXPANDED_DETECTION.md)**
Nine detection methods over the largest current catalogues, merged into
one organism list with one share of the whole per organism, competitive
confirmation and strain placement.
- **[Measured capability](MEASURED_CAPABILITY.md)**
What the detection found on simulated communities with known composition,
against the targets it was built to; stated as measured, not as claimed.
## The project
OpenBiota is free for any noncommercial purpose under the
[PolyForm Noncommercial License 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0);
commercial use requires a licence from OpenBiota. The website is
openbiota.com; the code lives on
[GitHub](https://github.com/openbiota-org/openbiota-gut-health-test). Add a
published study, improve an analysis, or make a finding easier to understand —
every contribution brings more of the world's microbiome research into a report
anyone can generate.
