Metagenomics - Powerful analyses of microbial communities

At GenoScreen, we turn metagenomic data into actionable insights through tailored analyses and cutting-edge scientific support.

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Why choose metagenomics?

Metagenomics allows the analysis of the diversity and functioning of microbial communities directly in their environment, without prior culturing. It offers a deep understanding of the composition, interactions, and functions of the microbiome, paving the way for major applications in human and animal health, dermocosmetics, environmental studies, and industrial biotechnologies.

Powerful analyses [...] Why choose metagenomics?

20+ years of experience

in genomics &
metagenomics

Metagenomics: Our Expertise

Our experience has allowed us to develop and refine robust methodologies tailored to the uniqueness of each sample type, ensuring the relevance and reliability of your results

You will be supported by a multidisciplinary team of experts in bioinformatics and microbiology, ensuring comprehensive and personalized project support.

Quality assurance, the core of our approach

We have implemented a systematic and thorough internal quality control system to validate the performance of our protocols and ensure the integrity of your results.

You will benefit from clear and interactive results, designed for in-depth understanding and optimal use of your data.

GCLP-compliant

rigorous &
traceable analyses

Methodologies adapted to every sample type

Each biological or environmental matrix is unique and requires a specific approach. Through our expertise, we have developed optimized protocols for various matrices:

Gut microbiota

Skin microbiota

Soils microbiota

Others

Other sample types? Our experience allows us to adapt our methods to a wide variety of samples.
Let’s talk about it!

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Our workflow applied to metagenomics

Optimized DNA extraction for each matrix

stool, soil, skin, fermented samples, etc.

Library preparation

with integrated quality controls

High-throughput sequencing adapted to your needs

Bioinformatics analysis

Interpretation & reporting

More technologies, more personalisation

We offer DNA sequencing technologies fully tailored to your analytical goals : Illumina (short-read) for high-throughput, accurate sequencing, and PacBio (long-read) for high-resolution insights, ideal for detailed microbial genome characterization.

Depending on the level of analysis required, our protocols are available in metabarcoding (16S, 18S, ITS) for a targeted approach, or shotgun metagenomics for a comprehensive exploration of microbial diversity, both taxonomic and functional.

Additionally, sequencing depth is adjusted to your specific needs, taking into account the richness and complexity of the microbiota under study(whether human, animal, plant, or environmental in origin).

Pricing

The GenoScreen experience in a nutshell...

From setting up your project to delivering the results

Methods and solutions tailored to your projects

Micro-organism studies for over 20 years

Support beyond results delivery

‘materials and methods’ explained

Targeted sequencing - An in-depth analysis of regions of interest

Targeted sequencing allows specific analysis of targeted genes (or gene regions) on many samples in parallel. With NGS sequencing on MiSeq^®, NextSeq500^® or Hiseq^® platforms, multiple genes can be evaluated with a smaller data volume, which is easier to manage and analyse than WGS datas.

Applications

Exome sequencing

This type of sequencing is essentially used to:

• Screen for mutations in genes involved in regulatory pathways
• Screen for mutations (SNPs, indels, etc.) associated with a particular disease (cancer, coagulopathies, etc.).

We use the NimbleGen SeqCap EZ protocol (Roche) for exome sequencing.

Personalized sequencing

After custom probe design, your regions of interest are enriched prior to sequencing which simplifies the subsequent data analysis. This protocol can be set up for any organism with an available reference genome.

GenoScreen's assets

• A dedicated team of scientists for each project.
• Comprehensive support with the elaboration of an experimental plan and project implementation.
• Assistance with data handling and interpretation of the results.

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Ready-to-load services - Plugged into our sequencing platform

For a cost effective and responsive offer, GenoScreen proposes "Ready to Load" sequencing services for a wide range of libraries: a real research accelerator giving the opportunity to perform on last generation technical platform with advanced expertise.

Applications

Transcriptomics - Analyzing gene expression

What is transcriptomics and why study it?

Transcriptomics determines which genes are actively expressed, to what extent under specific conditions. With high-throughput sequencing technologies, it provides a comprehensive and quantitative view of gene activity in both prokaryotic and eukaryotic organisms.

Today, transcriptomics is one of the most powerful methods to understand cellular responses to stress, treatments, environmental changes, or developmental stages.

Activ' Reveal

Our RNA-Seq applications

Our services cover all transcriptomic analysis needs:
- Differential expression analysis between conditions or treatments
- Transcript abundance quantification (mRNA)
- Functional gene annotation
- Detection of single nucleotide variants (SNPs) from transcripts
- Multi-omics integration with genomic or metagenomic data

Want to focus on a few genes of interest? We also offer targeted quantification via RT-qPCR, a fast, economical solution.

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RNA-Seq Workflow: from sample to results

Experimental design

RNA Extraction

Optimized protocols

Sequencing

Differential expression analysis

Comprehensive Reports (Physical & Summary)

ustom qPCR service comments workflow

Dedicated scientific team for each project.

Assistance in developing the experimental plan and sequencing strategy

Two methods are used to enrich the RNA fraction of interest (mRNA) prior to cDNA synthesis and library preparation:

- From total eukaryotic RNA: Capture of mRNAs by their polyA tail

- From total prokaryotic or eukaryotic RNA: Depletion of rRNA through capture by complementary probes. Enrichment of samples in mRNA

Comprehensive processing of sequencing data

Differential expression analysis

Functional enrichment analysis

Interactive reports for intuitive exploration of your data:

- Dynamic visualisations (graphs, tables)

- Filtering and sorting tools to target genes or metabolic pathways of interest

Interpretation of results and personalised support for independent use

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Whole-genome sequencing - A high-precision method for characterizing the genome

The latest sequencing technologies make it possible to analyze the full primary structure of an isolated organism’s genome, regardless of, whether the latter is a eukaryote, a prokaryote or a virus.
An analysis of whole-genome sequencing data provides a precised description of any type of organism and thus addresses a very broad range of research questions.

Applications

MLST/MLVA, microbial typing/tracing solutions

GenoScreen proposes you the opportunity to characterize more accurately your microorganisms (subspecies or strain characterization) using standardized and validated molecular biology methods such as MLST or MLVA (including MIRU-VNTR).

MultiLocus Sequencing Typing (MLST)

MLST/MLVA, microbial typing/tracing solutions - MLST

The MLST (MultiLocus Sequencing Typing) sequencing typing is the reference technique for the distinction of different strains. This method is based on the house-keeping genes sequencing (house-keeping genes are encoding essential proteins of the bacterium).

These sequences have the particularity of presenting a stable polymorphism over time and sufficient enough to distinguish strains from each other.

This approach allows the characterization of a microorganism whose genus (or species) is known in order to identity the species(or subspecies) and this thanks to the sequencing of 7 house-keeping genes.

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The MLST by GenoScreen

GenoScreen's MLST service offer is a complete package of services realized from extracted DNA or thermolysate. This includes the PCRs realization, the sequencing on a capillary sequencer, the sequences analysis and the strain assignment..

Multiple Loci VNTR Analysis (MLVA)

[EN] MLST/MLVA, microbial typing/tracing solutions - MLVA

The MLVA (Multiple Loci VNTR Analysis) is a genetic analysis method of VNTR (variable number of tandem repeats) pattern polymorphism based on their count. During a first step, each targeted VNTR locus is amplified by PCR with flanking-region specific primers. The fragments obtained are then separated according to their size by electrophoresis on capillary sequencer. The genotyping of each locus and the results compiled from each sample allow to assign to the strain a specific numerical code for a subspecies.

The MLVA approach allows to characterize a microorganism whose species is known, to identify, at least, the subspecies through allele typing and comparison to the MLVA databases. This method is more selective than the MLST method and does not require a DNA sequencing step. It thus makes it possible to differentiate close subspecies (clonal species).

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Le MLVA par GenoScreen

GenoScreen's MLVA service offer is a complete package of services realized from extracted DNA or thermolysate. This includes the PCRs realization, the electrophoresis on a capillary sequencer, the data analysis and the strain assignment. 

The analysis can be carried out on the basis of a personalised typing scheme tailored to your needs, in line with the data available for your species. 

SNP genotyping

This technique is based on the variation of a single nucleotide at a given position (Single Nucleotide Polymorphisms), which can lead to functional changes in the genes and proteins resulting from the modified amino acid sequence. By offering genome-wide analysis, GenoScreen can help you identify unknown genotype-phenotype associations or genetic variations that are already known.

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In what context should microsatellite genotyping be carried out?

Since SNPs can be found in any type of genome, genotyping them can be of interest in a wide range of applications. Our team is used to working on a wide range of problems, and can help you choose the best technique to meet your needs.

GenoScreen offer

Our services are tailored to your needs. We can use assays already available in databases, or identify and target SNPs of interest from sequencing data (with or without a reference genome).

Genotyping by qPCR

qPCR is used to identify genetic variations such as SNPs by specifically amplifying DNA sequences. This genotyping is based on methods such as TaqMan probes, which offer precise discrimination of alleles, or KASPar competitive PCR, which is more economical for large-scale or recurrent analyses.

These two methods for identifying genetic variants operated by GenoScreen will be proposed to you depending on the purpose and recurrence of your project. Our team can also help you design a genotyping kit.

 

 

A tailored approach to meet your needs

We work with you to plan all the stages required to bring your project to a successful conclusion, whatever your constraints in terms of number of samples or targets, timeframe and cost.

 

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Genotyping by sequencing

 

These technologies are commonly used in population genetics, conservation biology and ecology projects. It is not necessary to have access to a reference genome to carry out the analysis.

The data obtained can be used to identify SNPs as genetic markers, perform population structure and/or phylogenetic analyses.

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Sanger

Thanks to its reliability and accuracy, Sanger sequencing remains the reference method when it comes to verifying uncertain qPCR results or confirming mutations observed by high-throughput sequencing.