Human gut microbiome
Complete metagenomic sequencing of a stool sample: species-level taxonomy, resistome, virulence, functional profile and 8 clinical indices integrated into a single report. From data to clinical decision.
A single assay, complete coverage
Whole-microbial-genome shotgun sequencing overcomes the limitations of stool culture, PCR panels and 16S sequencing: it is not limited to who is there, but describes what they do and what risk they carry.
Taxonomic profile
~2,008 bacterial and archaeal species (Kraken2/Bracken + MetaPhlAn4). Enteropathogens (Salmonella, Shigella, Campylobacter, C. difficile, E. coli STEC/EIEC/ETEC) and opportunistic pathobionts.
Kraken2 · MetaPhlAn4Resistome (AMR)
Resistance genes for β-lactams (blaKPC, blaNDM, blaOXA, blaCTX-M), vancomycin (vanA/B), colistin (mcr) and linezolid, among other classes.
CARD 2025 · AMRFinderPlusVirulence and toxins
TcdA/TcdB and CDT of C. difficile, CPE and NetF of C. perfringens, Shiga toxin (Stx1/Stx2), cholera toxin, BFT/ETBF and cagA/vacA of H. pylori.
VFDB · 10 panelsFunctional profile
HUMAnN3 (ChocoPhlAn + UniRef90): butyrate and short-chain fatty acid synthesis, bile acid metabolism and MetaCyc pathways.
HUMAnN3Fungi, parasites and viruses
Mycobiome (Candida, Aspergillus, Saccharomyces), protozoa (Giardia, Cryptosporidium, Blastocystis) and enteric DNA viruses + phages.
Beyond bacteriaIndices + clinical triage
8 clinical indices with published AUC, severity triage (HIGH/MODERATE/INFORMATIONAL) and detection of pharmacological confounders.
GMHI · GMWI2 · EDS8 clinical indices
Each index is reported with its performance (AUC and 95% CI) so that the clinician knows exactly what to expect.
GMHI · GMWI2
Microbiome health indices (Gupta 2020; Chang/Gupta 2024), validated on thousands of metagenomes from dozens of countries.
DI V2 · EDS
Dysbiosis Index (z-score, 8:2 panel) and Enterotype Dysbiosis Score over 5 enterosignatures (Frioux 2023).
Butyrate Capacity
Butyrogenic capacity from 7 producer genera (Vital 2017), with interpretation bands.
CRC Risk
Species signatures enriched in colorectal cancer (Piccinno/Segata 2025): prioritization triage, not diagnosis.
IBD CD vs UC
Independent scores for Crohn’s disease and ulcerative colitis (Zheng 2024).
C. difficile Risk
Abundance, toxins and ecological environment associated with recurrence risk (IDSA/SHEA 2024).
When is it indicated?
Clear indications
Refractory IBS-D / IBS-M · CD vs UC characterization · recurrent C. difficile (≥2 episodes) · suspected SIBO · post-antibiotic dysbiosis with persistent diarrhea >2 weeks · chronic diarrhea with normal calprotectin and negative colonoscopy.
Also recommended
Supportive screening in FIT+ with deferred colonoscopy · monitoring of response to FMT · pre-immunosuppression evaluation · support for predicting response to immunotherapy · metabolic syndrome / T2D and the gut-brain axis.
From sample to report
1. Collection
At-home kit: DNA/RNA Shield tube + spatula. Fresh stool (2-5 g), no fasting.
2. Extraction and QC
Total DNA (ZymoBIOMICS), quantification and integrity control.
3. Sequencing
Shotgun PE150, ≥20 M reads (~6 Gb) with human read removal (GRCh38).
4. Report
14 sections, clinical indices, resistome and recommendations. Signed by a health biologist.
Sample and shipping
Fresh stool (2-5 g) in DNA/RNA Shield stabilizer (stable at room temperature for up to 30 days). Shipping with UN3373 label, prepaid envelope included. No fixatives.
Turnaround and delivery
Clinical PDF report within up to 30 days from receipt of the sample, downloadable from the portal. Includes interpretation consultancy and longitudinal follow-up.
Example reports
Real anonymized reports from different clinical profiles. Same format, same sections and the same level of detail you will receive.
Colorectal cancer screening
Male, 71 years old. Pre-therapeutic-decision screening; no high-priority pathogens and mild dysbiosis.
Report · PDFMetabolic profile
Male, 37 years old. Pre-intervention evaluation in a metabolic context with moderate-severe dysbiosis.
Report · PDFPediatric profile
Male, 12 years old. Pre-intervention evaluation in a metabolic context with mild dysbiosis.
Report · PDFFMT donor screening
Male, 32 years old. Verdict “NOT ELIGIBLE”: detection of pathogens that exclude donation.
Report · PDFActive ulcerative colitis
Female, 37 years old. Activity monitoring; the inflammatory clinical picture prevails over mild dysbiosis.
Report · PDFFrom raw data to clinical decision
A single stool assay: taxonomy, resistome, virulence, functional profile and clinical indices integrated.