Microbiome diagnostic panels

01Overview and value chain#

Markers EC: IVDR 2017/746 | OECD: Biotech-health | Regulator: FDA (USA), EMA (European Union), NMPA (China)

Microbiome diagnostic panels sequence and analyze the gut or gastrointestinal microbiome from a stool or swab sample, spanning consumer wellness testing at one end and clinical pathogen/dysbiosis diagnostics at the other. Viome offers an AI-powered “Full Body Intelligence” test that analyzes gut microbiome RNA expression to generate personalized health, aging and dietary insights for consumers. Codex Genetics runs a clinical metagenomic whole-genome-sequencing (WGS) platform with dedicated gastroenterological, gastric and metabolic diagnostic panels. Sequentia Biotech, based in Barcelona, Spain, recently achieved CE-IVD marking under the EU’s In Vitro Diagnostic Regulation (IVDR) for MICK Clinical, its bioinformatics software solution for gastrointestinal-pathogen detection — a real regulatory milestone for a clinically actionable microbiome diagnostic. In China, Realbio Genomics offers microbiome health-testing services as part of the country’s growing microbiome-testing base. In India, Yaazh Xenomics provides gut microbiome testing alongside broader microbial identification, metagenomics-analysis and bioinformatics services.

The key directions of microbiome diagnostic panels are:

1. Consumer wellness microbiome testing (Consumer Microbiome Testing): direct-to-consumer gut microbiome tests generating personalized health, nutrition and aging insights rather than a clinical diagnosis — Viome.
2. Clinical metagenomic diagnostic panels (Clinical Metagenomic Panels): dedicated gastroenterological, gastric and metabolic metagenomic sequencing panels used in clinical diagnostic workflows — Codex Genetics.
3. Bioinformatics-driven GI pathogen detection (Bioinformatics GI Diagnostics): regulatory-cleared software analyzing microbiome sequencing data to detect gastrointestinal pathogens for clinical use — Sequentia Biotech’s MICK Clinical.
4. Regional microbiome testing services (Regional Microbiome Testing): domestic microbiome sequencing and testing services adapted to a local market and regulatory pathway — Realbio Genomics, Yaazh Xenomics.

Sectoral value chain#

[sample collection (stool/swab)] ──> [sequencing/metagenomic profiling] ──> [bioinformatics taxonomic/functional analysis]
                                                    │
                                       (report generation: health or diagnostic)
                                                    │
                                                    ▼
[clinical or consumer action] <─── [regulatory clearance (where clinical)] <─────┘

Value chain levels#

Cross-cutting technologies of the sector:

• Shotgun metagenomic sequencing (Clinical Metagenomic Panels): untargeted sequencing of all microbial DNA in a sample identifies the full community composition, including pathogens a targeted panel might miss.
• RNA-based microbiome activity profiling (Consumer Microbiome Testing): analyzing microbial RNA expression (rather than DNA presence alone) captures which microbial functions are actively occurring, the basis of Viome’s health-intelligence scoring.
• Bioinformatics pathogen-detection software (Bioinformatics GI Diagnostics): regulatory-cleared analysis software processes microbiome sequencing data to flag clinically actionable gastrointestinal pathogens, as Sequentia Biotech’s IVDR-cleared MICK Clinical does.

02US#

The US spans both ends of the microbiome-testing spectrum, from Viome’s consumer wellness platform to Codex Genetics’ clinical metagenomic diagnostic panels.

Viome, Codex Genetics, FDA#

• Viome: offers an AI-powered “Full Body Intelligence” test analyzing gut microbiome RNA expression to generate personalized health, aging and dietary insights for consumers, marketed as a wellness rather than diagnostic product.
• Codex Genetics: runs a clinical metagenomic whole-genome-sequencing platform with dedicated gastroenterological, gastric and metabolic diagnostic panels for clinical use.
• FDA framework: clinical microbiome diagnostic panels reach the US market predominantly as laboratory-developed tests (LDTs) under CLIA, while consumer wellness tests like Viome’s generally fall outside FDA diagnostic-device regulation as non-diagnostic products.

03CN#

China hosts a growing domestic microbiome-testing base, with Realbio Genomics among the active providers of microbiome health-testing services.

Realbio Genomics, NMPA#

• Realbio Genomics: offers microbiome health-testing services as part of China’s growing microbiome-testing base.
• NMPA framework: clinical-use microbiome diagnostic panels in China require NMPA approval as in-vitro diagnostic products, while consumer wellness-oriented tests generally face lighter regulatory requirements.

04EU#

Spain anchors a clinically significant EU entrant through Sequentia Biotech’s IVDR-cleared gastrointestinal pathogen-detection software.

MICK Clinical, IVDR#

• Sequentia Biotech (Barcelona, Spain): recently achieved CE-IVD marking under the EU’s In Vitro Diagnostic Regulation for MICK Clinical, its bioinformatics software solution for gastrointestinal-pathogen detection from microbiome sequencing data — a real clinical-diagnostic regulatory milestone in this category.
• IVDR framework: clinical microbiome diagnostic software and panels sold in the EU require conformity assessment and CE marking under the In Vitro Diagnostic Regulation (IVDR 2017/746), the bar MICK Clinical has cleared.

05Leading companies and research institutes#

06Tech stack and innovations#

The stack spans consumer-facing RNA-based wellness scoring, clinical shotgun-metagenomic diagnostic panels, and regulatory-cleared bioinformatics software that turns raw sequencing data into a clinically actionable pathogen call.

1. AI-powered RNA-based wellness scoring (Consumer Microbiome Testing):
   • Viome’s Full Body Intelligence test analyzes gut microbiome RNA expression with AI-driven scoring to generate personalized health, aging and dietary recommendations for consumers.
2. Clinical metagenomic panels (Clinical Metagenomic Panels):
   • Codex Genetics’ dedicated gastroenterological, gastric and metabolic metagenomic WGS panels give clinicians pathogen and microbial-community data for specific disease-area workups.
3. Regulatory-cleared pathogen-detection bioinformatics (Bioinformatics GI Diagnostics):
   • Sequentia Biotech’s MICK Clinical software achieved IVDR CE marking for gastrointestinal-pathogen detection, demonstrating that microbiome bioinformatics can clear the same clinical-diagnostic regulatory bar as a conventional assay.
4. Regional microbiome testing capacity (Regional Microbiome Testing):
   • Realbio Genomics and Yaazh Xenomics build domestic microbiome-testing capacity adapted to their respective markets in China and India.

07Value chains and production pipelines#

Industrial pipeline of a microbiome diagnostic panel (FDA LDT / EU IVDR 2017/746)#

┌───────────────────────────┐      ┌───────────────────────────┐
│ 1. Sample collection      │ ───> │ 2. Sequencing &           │
│                            │      │    metagenomic profiling    │
└───────────────────────────┘      └───────────────────────────┘
                                                   │
                                                   ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 4. Report generation      │ <─── │ 3. Bioinformatics         │
│                            │      │    analysis                 │
└───────────────────────────┘      └───────────────────────────┘
              │
              ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 5. Regulatory clearance   │ ───> │ 6. Clinical/consumer      │
│    (where clinical)        │      │    action                   │
└───────────────────────────┘      └───────────────────────────┘

Stage 1: Sample collection

The consumer or patient collects a stool or swab sample using a provided kit, then ships it to a central sequencing lab.

Stage 2: Sequencing and metagenomic profiling

The lab performs shotgun metagenomic or targeted sequencing of the microbial DNA/RNA present in the sample, generating raw sequence data covering the full microbial community.

Stage 3: Bioinformatics analysis

Taxonomic classification and functional-pathway analysis convert raw sequence data into a microbiome composition profile, or, in the case of Sequentia Biotech’s MICK Clinical, a specific pathogen-detection call.

Stage 4: Report generation

A consumer-facing wellness report (Viome) or a clinical diagnostic report (Codex Genetics, Sequentia Biotech) is generated from the analysis, tailored to the intended use case.

Stage 5: Regulatory clearance (where clinical)

Clinical-use panels require FDA LDT/CLIA status, EU IVDR CE marking, or NMPA approval before clinical adoption; consumer wellness tests generally market outside this diagnostic-device regulatory scope.

Stage 6: Clinical or consumer action

A clinician acts on a pathogen or dysbiosis diagnosis to guide treatment, or a consumer adjusts diet and lifestyle based on the wellness insights returned by a test like Viome’s.