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DNA/RNA extraction

Given the fact that molecular analyses of bacterial communities are based on DNA and/or RNA, the extraction of these molecules from the initial sample represents a critical step. The DNA and RNA extraction methods must be as stable and unbiased as possible, because the objective is to study the microbiota inside its initial ecological niche and to obtain the most stable and exhaustive profile possible.

GenoScreen - Services provided

To obtain reliable, precise descriptions of microbiotas and, to reduce bias, GenoScreen has developed standardized, optimized extraction processes for the following microbiotas:

• Human or animal microbiotas (feces, caecum/ileum samples, skin swabs).
• Microbiotas in the environment (agricultural soil, polluted soils, rhizospheres).

GenoScreen can also provides support for DNA extraction from various samples, such as skin/intestinal biopsies, oral/nasal swab samples, sputum, bronchoalveolar lavage, surface water, groundwater etc.

GenoScreen's assets

• 15 years of experience in the extraction of DNA from all types of matrix.
• Maximized repeatability and reproducibility.
• Extraction processes specifically optimized for microbiotas.

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Metatranscriptomics - An analysis of enzymatic functions and metabolic pathways

The metatranscriptome corresponds to the whole set of genes and functions expressed (i.e. the transcriptomes) by the microorganisms in a sample.

Applications

Metatranscriptomics opens up many fields of analysis:

• The identification of expressed enzyme functions and metabolic pathways.
• Comparisons of gene expression levels between samples or experimental conditions.
• The identification of microorganisms involved in the expression of metabolic pathways of interest.

GenoScreen - Services provided

The GenoScreen teams can investigate the initial matrix by extracting all the RNA produced by the microorganisms present in the sample.

The library preparation methods are then adapted to match the research objectives and the nature of the initial matrix:

• For eukaryotes
  
  • Specific enrichment of poly(A) mRNA.
• For bacteria
  
  • Removal of eukaryotic poly(A) mRNA.
  • Subtraction of very strongly expressed ribosomal RNA.

GenoScreen's assets

• Full project support, from the collection of the initial samples to the preparation of RNA-Seq libraries.
• Customized sequencing strategies (depending on the number of samples and the sequence length, etc.).
• 15 years of expertise in RNA analysis.
• Expertise in transcriptomics.

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Shotgun metagenomics - A non-targeting approaches

As a complement to targeted approaches (which examine small, specific regions of ribosomal genes), this metagenomics approach is based on the shotgun sequencing of all the DNA extracted from a sample.

This analysis allows to describe the taxonomy, diversity, genes and functional capacities of a community of organisms. It can also, usefully, complement profiling studies (e.g. on a representative sub-group of samples).

Applications of shotgun metagenomics

Shotgun metagenomics can add an important value in developing soil remediation methods, new antibiotics and new enzymes for improved industrial and agricultural processes.

GenoScreen - Metagenomics services provided

GenoScreen provides very flexible analytical services according to your project, your initial matrix and the required sequencing coverage. Depending on your needs, research issues and constraints, you can choose between our low-, medium- and high-throughput whole metagenomics sequencing analyses (WHOMSA^®).

Our teams use powerful bioinformatics tools (WHORMSS^®) to extract as much value as possible from the huge volume of data collected. These exclusive tools can be adapted to address many different research issues and then provide you with specific answers.

GenoScreen's assets

• A high flexibility service provider.
• Complementary targeted and Shotgun metagenomics analyses.
• A proprietary bioinformatics tool (WHORMSS^®).

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Detection and quantification of specific bacteria in communities

As a complement to NGS-based approaches, such as microbial profiling or to target specific bacterial families or species (e. g. probiotics), quantitative approaches that analyze changes in relative abundance are also possible.

Applications

This approach can considerably be used to confirm the observations made by targeted metagenomics : this is a very useful tool in the agrifood sector (checking the inoculum and the presence of bacteria in the fermentation process or checking formulas, i.e. the presence of probiotics or prebiotics).

GenoScreen -  Bacteria detection and quantification services provided 

GenoScreen develops quantitative PCR (qPCR) assays for the detection and quantification of specific probiotic bacteria in complex matrices:

• Lactobacillus casei
• Lactobacillus rhamnosus GG
• Lactobacillus acidophilus
• Enterococcus faecium
• Bifidobacterium lactis (BB12)
• Streptococcus thermophilus
• Staphylococcus cerevisiae/boulardii
• Escherichia coli...

GenoScreen is continually expanding its offer of species-specific qPCR assays.

We can also provide custom services and validate qPCR assays on demand for the targets not including in the catalog.“

Do not hesitate to contact us for more information about our updates or any other specific inquery.

GenoScreen's assets

• A catalog of deviserified specific qPCR assays.
• Development and validation of qPCR assays on demand.

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Molecular biomass analysis

Molecular biomass represents the quantity of DNA extracted from a given sample. It provides an estimate level of diversity in living microorganisms in a given habitat, sample or environment and enables it to be compared to others.

Applications

This type of analysis has many applications in healthcare, environmental and agrifood sectors.

It, notably, provides a fast analysis (with any type of sample) of the impact of a drug (antibiotics, chemotherapy, etc.), a pollutant or a change in a manufacturing process on microbial diversity.

GenoScreen - Services provided

Our DNA analyses are based on targeted quantitative PCR methods that distinguish between prokaryotes and eukaryotes.

GenoScreen also detains exclusive technologies to specifically identify fungi.

In addition to these whole-sample analyses, our scientific staff has developed targeted, quantitative assays for various bacteria of interest (Lactobacillus casei, Bifidobacterium lactis, Faecalibacterium prausnitzii, etc.).

Other assays can be developed on a custom basis or on request, depending on the issue to be addressed.

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Microbial communities

Consisting in bacteria, archaea, protists, fungi and/or viruses previously unknown, microbial or microbial communities are now recognized as key actors in the proper functioning of our organism and our environment. Since 2008, GenoScreen has a particular focus on the study of these microbial communities and its R&D team has developed, optimized and standardized various methodologies mandatory for their study (Metabiote^®, WHORMSS^® etc), starting with the extraction of gDNA adapted to different samples of human/animal microbiotes (faeces, skin samples, oral, sputum, intestinal biopsies etc.) or environmental microbiotes (agricultural/polluted soils, rhizospheres, filtered air etc.) to the final metadata analysis.

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