Microbial flora
The analysis of microbial communities (microbiotas)
A microbiota analysis provides information on the entire set of microorganisms (bacteria, yeasts, fungi, algae, etc.) present in a given sample.
This type of analysis is now crucial in the evolution of research in human and animal health, nutrition, environment and biotech.
As a leading provider of genome analysis services, GenoScreen provides powerful, comprehensive solutions for microbiota analysis that will boost your research and give you huge beneficial options in genomics of the future!
Understanding whole ecosystems on the molecular scale
When compared with conventional microbiological tests, molecular analyses of microbial communities are, above all, useful in the study of microorganisms within their ecological niches, i.e. in the absence of culture steps in artificial media that separate the microorganisms from their community and their natural environment.
These microbial ecology analyses provide information on biomass, composition, diversity, functions, interactions between microorganisms and interactions with their habitat.
Bacterial and fungal profiling via targeted metagenomics - Speed and precision
The advent of next-generation sequencing technologies has revolutionized molecular approaches aiming to describe the diversity and taxonomic composition of a microorganism-containing sample. In fact, this type of analysis used to be based on the analysis of the rRNA16S and rRNA18S/28S genes using PCR amplification, cloning and Sanger sequencing. These approaches were time-consuming, fastidious and, often, provided information only on the most prevalent microorganisms in a sample.
Today, targeted metagenomics and microbial profiling approaches performed on NGS systems are replacing older methods and are generating far more sequence data per sample than could previously be envisaged.
GenoScreen - Bacterial and fungal services provided
Our methodology is still based on the targeted analysis of ubiquitous genes (rRNA16S, rRNA18S/28S, ITS1&2), which are now directly obtained using next-generation sequencers.
In addition to a taxonomic analysis, our teams can offer more in-depth outputs (beta diversity, phylogenetic trees, etc.).
Metabiote: the benchmark in targeted metagenomics
GenoScreen has developed a standardized, optimized metagenomics technique that incorporates all our expertise. Metabiote® limits methodological bias and thus enables comparisons of microbial diversity across cohorts of samples :
- Limited PCR biases during sample preparation
- Guaranteed repeatability and reproducibility
- Integrated quality controls throughout the process
- Fully automated data analysis
- GCLP compliant protocol
GenoScreen's assets
- Pioneer in NGS technologies in France.
- Ten years of experience in the field of targeted metagenomics.
- In-depth experience of many initial matrices (stools, skin swabs, etc.).
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.
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.
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®).
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.
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.