GenoScreen Expertise

Analysis and characterization of cutaneous microbiomes

The skin's microbiota is made up of billions of microorganisms, covering various species, living in community and closely linked to skin health. Increasingly, the microflora is being studied using genomics solutions, and GenoScreen has developed a complete solution for analysing the skin microbiome. These technologies open up new prospects for the development of cosmetics, skincare products and personalised treatments for atopic skins.

What genomics can bring to skin microbiota understanding ?

Metagenomics is the most complete and cutting-edge approach for characterizating and studying microbiomes, allowing to have a global overview of microorganisms in presence in any sample, and their functional potential.

GenoScreen intervenes at different steps of any research and development project on skin microbiome. Our genomic solutions cover the following purposes :

• Studies of the impact on skin microbiota of skincare product or active ingredient
• Dermatology and Clinical studies in dermocosmetics to assess treatments effects on skin diseases
• R&D exploratory projects focusing on skin microbiota
• Proofs of concept of active ingredients effects on cutaneaous microorganisms
• Scientific communication support with ready-to-publish results
• Claim validation, scientific based, to ensure product interaction with skin microbiome
• Substantiation of « microbiome friendly» claims, proving that the concerned cosmetic product doesn't harm the consumer microbiota and his epidermis health
• Prebiotics, Probiotics, Postbiotics ingredients testing
• Microbial communities exploratory studies throughout R&D collaboration for biomarker detection and focused analysis for instance.

Our solutions for skin microbiome testing and analysis :

From your biological question to its technological answer, we bring together our technologies and know-how to offer the best solution fitting your project.

Mainly performed on in-vivo human samples, our analysis can be conducted with other models (in-vitro synthetic reconstructed human epidermis, ex-vivo explant tissue cultures).

Metagenomics

The key to understand interactions between the epidermis and its microbial flora.

• Short read targeted metagenomics : The first step into cutaneous microbiota analysis. Supported by an Illumina sequencing platform, short read metagenomics provides an overview of the taxonomic genera present in skin swabbing samples. The identification of cutaneous microflora relies on 16S rDNA sequencing for bacterial targets or 18S/ITS rDNA regions for fungal targets.

• Long read targeted metagenomics : The most appropriate solution for skin microbiome analysis and characterization. Long read metagenomics allows to go further in taxonomic identification, to the species level. A significant advantage when it comes to distinguishing species that are important for skin health. Based on either PacBio or Oxford Nanopore Technologies platforms, it enables a more detailed comparison between the samples.

• Shotgun Metagenomics : Sharp and complete description of all microorganism's genomes in each sample. Shotgun metagenomics provides skin microbiome functional potential, beyond the characterization of all species in a single analysis such as prokaryotes (bacteria, yeasts and other Fungi) and small eurkaryotes. Thanks to Next Generation Sequencing (NGS) on an Illumina platform, this non-targeting approach offers a global overview of the genomes of all organisms constituting the cutaneous microbiota and gives access to relative value quantification of their content and proportions in each sample. With this technology, gene annotation is permitted.

• • Taking into account all microorganisms (all domains, kingdoms and genera combined) in a single analysis
  • Relative quantification of samples’ population
  • Global and complete overview of microbiota’s genome
  • Gene annotation
  • Skin microbiome functional potential

Bioinformatics

• Technical expertise

Our bioinformatics platform works on databases and pipelines specific to the skin microbiomes, developed in-house, allowing powerful analysis of microbial communities.

• Decoding skin microbiome

We supply through interactive reports, a complete picture of cutaneous microbiota, integrating, among other parameters, the following : alpha-diversity, beta-diversity, samples distance and composition comparison.

• Easy to use interface

The interface is both interactive for the user, and on the other hand built on a scientific format, making it easy to understand the content, and suitable for its use into scientific publications and communication clinical studies or regulatory files.

qPCR approach

Design of specific primers for any species or strains, and probes for their quantification in all kind of samples : in vivo , ex vivo , in vitro.

Quantitative real-time PCR allows fast and robust assessment of the effects of different skin care products applications on cutaneous microbiota.

GenoBiome^® Skin

All-in-one solution for in vivo skin microbiome analysis, adaptable to each project, with support and expertise from our team of microbiologists, genomic experts and bioinformaticians. GenoBiome^® Skin is based on a complete pipeline, from the experimental protocol design with our experts, through sequencing and bioinformatics data processing, to the delivery and interpretation of results. A broad range of technological answers applies in the frame of GenoBiome^® such as our metagenomic portfolio and strain-specific customized analysis, constituting the most advanced solution to support your research and development projects on skin microbiota.

• Experimental design for in vivo studies
• Cutaneous sampling standardized protocol
• Supply of collection material (swabs)
• Storage and shipment protocol
• Customized analysis pipeline with low biomass extraction methods and optimized sequencing strategy
• Curated bioinformatic tools and databases for skin microbiome analysis
• Interactive reports, ready-to-publish
• Results interpretation : more than data, answers to your biological questions.
• Support and guidance through the entire process, with regular milestones follow-ups

Interested in our solutions for your project? Contact us and indicate us your future study’s parameters, such as : number of samples, initial protocol (sampling frequency), selected panel, aim of the study (biological question), answer sought and associated technology (which level of analysis are you interested in). Our teams will provide you with a fast and appropriate response.

This email address is being protected from spambots. You need JavaScript enabled to view it. 

By applying a broad panel of genomic technologies and services, GenoScreen provides various solutions in identifying microorganisms via DNA sequencing and comparison with international databases.
These powerful and precised solutions are able to identify and characterize the microorganisms of interest: the species, the sub-species or the strain, typing, tracking and antibiotic resistance.

Identification and characterization

In order to identify a specie, ribosomal DNA regions targeted are adapted to each microorganism.

Additionally, to refine and adapt the identification to your needs, other genomic targets (rpoB and gyrB genes, etc.) are then used (discrimination within a group of species sharing the same ribosomal DNA sequence, for example).

GenoScreen can also leverage its know-how in whole-genome sequencing for a more precised characterization of a strain : virulence, antibiotic resistance, genomic comparisons with the strain library, etc.

Microbial typing and tracking

Our solution precisely characterizes any microorganism at the sub-species or strain level by using standardized, validated molecular methods, such as multilocus sequence typing (MLST) and multiple loci VNTR analysis (MLVA).

The typing schemes in open-access databases (PubMLST, MLST.org and MicrobesGenotyping) are used as references for these analyses.
The analysis can also be performed on a custom typing scheme.

Antibiotic resistance

GenoScreen determines antibiotic resistance profiles via targeted sequencing of genes known to be associated with antibiotic resistance or by whole-genome sequencing. The sequences are compared with open-access databases or the literature data.

In-depth NGS sequencing can detect the presence of low-frequency variants conferring resistance (heteroresistance).

An expertise in the genomic characterization of microorganisms

As an international specialist in microbial genomics, GenoScreen develops fast and precised solutions for characterizing, tracking and typing isolated microorganisms (bacteria, fungi, yeasts, etc.) and analyzing complex microbial florae:

• Scientific and technological services with a high level of expertise.
• Research under contract.

These advanced analytical strategies address many research issues in healthcare and environmental sectors. These techniques can identify, track and characterize microorganisms on the individual or community scale in order to understand their positive or negative impacts on health, safety and well-being of humans, animals and environment.

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.

Ask for a quotation

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.).

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.).

Ask for a quotation

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.

Ask for a quotation