Documentation

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.

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)

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

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 and the NO WARRANTY, NO MEDICAL ADVICE, NO LIABILITY section of the licence.

Where to start

• Quickstart

  From a fresh clone to your first PDF: tools, reference data, one command.

• Installation

  macOS and Linux, the two MetaPhlAn environments, verifying the install.

• Usage

  Every openbiota command and flag, caching, performance tuning.

• Reading the report

  What each section means, the seven-band scale, results.json.

• Method

  How the measurements are made and why they are made that way.

• Validation

  Sensitivity, specificity, the reference cohort, and a like-for-like comparison against a commercial report.

• Organism detection

  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

  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; commercial use requires a licence from OpenBiota. The website is openbiota.com; the code lives on GitHub. 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.