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GENXMAP
GENXMAP
GENXMAP
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Metagenomics Package

A comprehensive exploration to unveil the secrets of life.

Metagenomique-Genxmap

3

Analysis levels included: taxonomic, functional, and comparative

98%+

Taxonomic coverage across known microbiomes

+150

Functional gene detection per sample (average)

Our Metagenomic Sequencing Plans
Packages (Standard):

  • 16S rRNA gene / 18S rRNA gene

  • Shotgun

  • Metatranscriptomics

Projects (Custom):

  • Fungal ITS

  • Long Reads

Why Choose Our Metagenomics Package?
✅ A modular approach tailored to your objectives
✅ Custom scientific support for every project
✅ Capability to handle complex samples with reliability
✅ Clear, flexible deliverables adapted to your needs

Unveiling microbial worlds, powering innovation

Overall Vision

A global approach to exploring the genetic diversity of human and environmental microbiota.

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Metagenomics makes it possible to analyze the entire genetic material of a microbiota, whether intestinal, skin-related, or environmental.

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It reveals the taxonomic and functional diversity of microbial communities without the need for culture, making it a powerful and unbiased method for characterizing the microbial ecosystem as a whole.

The GENXMAP Approach & Technologies

Cutting-edge technologies for comprehensive and accurate profiling
 

At GENXMAP, we combine our scientific expertise with advanced sequencing technologies to provide exhaustive and actionable analysis of your microbial samples:

✔ Taxonomic profiling of microbial communities through 16S rRNA sequencing for prokaryotes (e.g., bacteria, archaea) and 18S rRNA sequencing for eukaryotes (e.g., fungi, protozoa).
✔ In-depth functional analysis using Shotgun sequencing, enabling the exploration of coding genes and active metabolic pathways within samples.

Applications and Fields

Cross-disciplinary expertise for health, environment, and applied research

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Metagenomic approaches are essential across multiple domains:

  • Human health: understanding of the intestinal, skin, oral, and vaginal microbiota

  • Environment: analysis of soils, waters, biofilms, effluents, etc.

  • Biotechnologies: identification of enzymatic and metabolic functions, as well as resistomes

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The microbiota plays a key role in homeostasis, pathologies, treatment response, and host–environment interactions. Yet, many microbial functions remain unknown, paving the way for new scientific discoveries.

Clear insights, actionable data

Turn microbial complexity into actionable insights

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With our standardized protocols, bioinformatics pipelines, and clear reporting, you gain a deep, interpretable, and actionable understanding of the microbial communities within your samples.

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Our metagenomic solutions are designed to support your research, diagnostic, or innovation projects — from DNA extraction to final data delivery.

Microbe discovery and classification

Explore the invisible. A bespoke metagenomic solution to uncover and characterize microbial diversity with accuracy.
1. DNA / RNA Extraction"

Obtain high-quality DNA extracts, tailored to your metagenomic applications

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Applications:

  • DNA extraction from diverse matrices (soils, water, tissues, feces, biofilms, etc.)

  • Quality and concentration verification of DNA extracts prior to sequencing

  • Targeted or shotgun metagenomic analyses

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Techniques:

  • Optimized extraction kits with protocols adapted to sample type and analytical objectives

  • Nanodrop: rapid measurement of DNA concentration and purity (260/280 and 260/230 ratios)

  • Qubit: sensitive and precise quantification, ideal for low concentrations

  • Fragment Analyzer / TapeStation: assessment of DNA integrity

2. Library Preparation and Quality Control

Prepare your metagenomic libraries and ensure their quality for high-performance sequencing

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Applications:

  • Preparation of samples for metagenomic sequencing

  • Verification of library quality and fragment size

  • Evaluation of concentration prior to sequencing

  • Quality control of amplified libraries

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Techniques:

  • Fragment Analyzer / TapeStation: assessment of library size and quality, detection of profiles and potential dimers

  • Qubit: precise quantification of libraries for optimal sequencing loading

  • Library-specific qPCR: functional quantification of sequencing-ready libraries, ensuring optimal yield

3. Next-Generation Sequencing (NGS)

Perform your NGS sequencing on MiSeq and NovaSeq with reliable results and rigorous quality control

Applications:

  • Targeted sequencing of 16S, 18S, or ITS regions

  • Shotgun metagenomic analyses

  • Environmental and clinical microbial monitoring

  • Study of microbiota and complex microbial communities
     

Techniques:

  • MiSeq (Illumina): high-throughput sequencing platform suitable for small to medium-scale projects, with short- to mid-length reads (2×150 bp to 2×300 bp)

  • NovaSeq (Illumina): ultra-high-throughput sequencing platform designed for large-scale projects requiring massive coverage and high data volumes

Our Ready-to-Use Packages

Optimized, ready-to-use workflows...
Our solutions, your project!
Package 16S-18S-Genxmap
Metagenomic Sequencing Package — 16S/18S
Check our shop for pricing and ordering options.
*For any order ≥ 48 samples

Proposed Configuration

  • Target: 16S rRNA gene or 18S rRNA gene

  • Samples: Intestinal, skin, and environmental microbiota (soil, water, air)

  • Methodology:

    • DNA extraction

    • Post-extraction quality control (quantity, purity, integrity)

    • Targeted PCR: 16S (V3–V4) and/or 18S (V4)

    • Library preparation: dual indexing

    • Sequencing: Illumina MiSeq 2×250 bp
       

  • Bioinformatics: QC/filtering → Denoising/Clustering → Taxonomy assignment (SILVA 16S/18S) → Basic alpha/beta-diversity + PCoA → ASV & taxonomy tables by marker + combined export

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  • Deliverables: FASTQ files + QC reports; ASV & taxonomy tables (CSV/BIOM); barplots/heatmaps/PCoA; PDF summary report

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Options: ITS1/ITS2 (fungal profiling), other regions (16S V1–V3, V4–V5; 18S V9), increased depth/subsampling, metadata co-analysis, functional prediction

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Package Shotgun-Genxmap
Metagenomic Package — Shotgun
Check our shop for pricing and ordering options.
*For any order ≥ 12 samples

Proposed Configuration
 

  • Target: Complete microbial genome (bacteria, archaea, viruses, unicellular eukaryotes)

  • Samples: Intestinal, skin, and environmental microbiota (soil, water, air), agri-food samples

  • Methodology:

    • DNA extraction

    • Post-extraction quality control (quantity, purity, integrity)

    • Shotgun library preparation (fragmentation, end-repair, dual indexing)

    • Sequencing: Illumina NovaSeq / NextSeq (2×150 bp, 12 Gb)
       

  • Bioinformatics: QC/filtering → host DNA removal → de novo assembly and/or binning → taxonomic annotation → functional annotation → comparative analysis → visualization of results
     

  • Deliverables: FASTQ files + QC reports; annotated assemblies/bins; comparative tables (CSV/BIOM); visualizations (barplots, heatmaps, PCoA, functional networks); PDF summary report
     

Options: Increased depth / ultra-deep sequencing; multi-group comparative analysis; co-analysis with clinical or environmental metadata; targeted focus; RNA extraction → shotgun metatranscriptomics (active functional profiling)

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Package métatranscriptomique-Genxmap_edited.jpg
Metatranscriptomics Package
Check our shop for pricing and ordering options.
*For any order ≥ 12 samples

Proposed Configuration

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  • Target: Total microbial RNA (expressed mRNA, rRNA-depleted)

  • Samples: Active microbiota (gut, skin, soils, biofilms)

  • Methodology:

    • Microbial RNA extraction

    • Post-extraction quality control (quantity, purity, integrity; RIN ≥7)

    • rRNA depletion

    • RNA-seq library preparation

    • Sequencing: Illumina NovaSeq 6000 (2×150 bp, ~20M reads/sample)

 

  • Bioinformatics: QC/filtering → microbial transcriptome assembly → functional annotation → expressed gene quantification → active metabolic pathway analyses → visualization of results

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  • Deliverables: FASTQ files + QC reports, gene/pathway expression matrices, functional profiles (heatmaps, PCoA, enrichment analyses), PDF summary report

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Options: Multi-omics integration (DNA + RNA), increased sequencing depth, differential analyses (treatment response, experimental conditions), post-analysis meeting (60 min) for results presentation and discussion

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Kickstart your project today

Tell us what you need — we’ll get back to you with a bespoke solution.

Our DNA

We leverage our expertise and technologies to help our partners and clients turn biological complexity into reliable, actionable data.

From method to impact

Discover how we work at GENXMAP

Our solutions

Precise and advanced services, cutting-edge technologies, and reliable analyses.
Our rigorous approach ensures detailed results, essential for your scientific discoveries and clinical applications.

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