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PHYLOGENE SA

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BERNIS, FR

About PHYLOGENE SA

Phylogene SA was launched in 1999 with the objective of developing methods of identification and ways to authenticate, using DNA and proteins. The applications are mainly the service to the food industry, health industry including in vitro diagnostics, cosmetics, environment industry as expertise or analysis and as kit developer to the diagnostics industry.

Our Services (13)


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Proteomics

Price on request

HolXplore: Global analysis of the human proteome and metaproteome of the associated microbiota.
HolXplore is a complementary analysis of data from metaproteomic experiments, highlighting the biological effects related to the results:

LEVEL 1 Taxonomic analyzes.
- Analysis of the diversity of the microbiota associated with the 2 conditions tested.

- Evaluation of a potential change in microbiota structure at different taxonomic levels, validation by statistical analysis.

- Dispersion of samples according to the diversity of their microbiota.

LEVEL 2 Functional Analyzes
The following analyzes will be carried out in parallel for the taxa 1) Bacteria, 2) Fungiet 3) Homo sapiens:

Research of orthologues and functional categories and associated general COG processes.
Determination of potential significant evolutions at different functional levels (terms, functional categories, general processes).
Involvement of protein orthologs in KEGG pathways.
Dispersion of samples according to the bacterial, fungal or human proteome.
LEVEL 3 Correlations / Claims
Dispersion of samples according to bacterial, fungal and human proteomes.
Calculation of correlation coefficients between different functions.
Calculation of correlation coefficients between different functions and taxonomic groups.
Involvement of orthologs of bacterial, fungal and human proteins in KEGG pathways.
Claims / Biological effects possible on the collection of the host and its microbiota.


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Microbiome Studies

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We offer three types of study services in substantiation, on host side, microbiome side and host+microbiome side simultaneously

Follow-up by quantitative PCRs of major species or genus, for example Staphylococcus sp. (Firmicutes), Corynebacterium sp. (Actinobacteria), Propionibacterium sp. (Actinobacteria) . Other targets are possible depending on wished effects from product positioning, also at species level.
Gives answer such as «  the product has/does not have an effect on tested genus » .
Time to delivery : 2 weeks for 5 genus or species, 5 samples compared to 5 controls (10 tests) preocessed together
Metagenomics comparative study of microbiome by NGSequencing 16S rDNA.
Gives answer in a report as : « The product/treatment does or does not impact the semi-quantitative composition and microbiome diversity».
Time to delivery  : Around 2 months for 5 samples compared to 5 controls (processed together)
Metaproteomics comparative study  of microbiome by relative quantification LC-MS/MS « shotgun proteomics » and bioinformatics/biostatistics dedicated data processing and analysis for microbiome :HolXploreTM
Gives answer in a report as : “ Effects of the product on functions and interactions of host and microbiome simultaneously ”
Time to delivery : Around 8 weeks for 5 samples compared to 5 controls (processed together) by LC-MS/MS, 5 weeks for HolXploreTM
Metagenomics and metaproteomics studies may be coupled in order to get a better database targeting


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Proteomics Data Analysis

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CORAVALID: Complementary analysis of relative quantification data in the comparison of two proteomic conditions.
LEVEL 1: Enrichment Analysis
The basic version of CORAVALID is a complementary analysis of the data, highlighting the biological processes, molecular functions, cellular components and metabolic and signal pathways related to proteins or genes significantly regulated in a quantitative comparison in high resolution proteomics or in genomics (" biochips ").

The associations are validated by statistical tests and manual curation.

LEVEL 2: Synthesis and interpretation
The standard version of CORAVALID Level 2 synthesizes and interprets these results and the information associated with each protein, to highlight the phenomena and mechanisms at work distinguishing the two samples compared. This synthesis makes it possible to highlight the major biological functions impacted.

Contextualization and / or follow-up meeting if desired

LEVEL 3: Biological Meanings - Proposed Claims
A selection of the major impacted biological functions is performed to determine if they are positively or negatively regulated. This choice takes place during the contextualization and / or follow-up meeting. In the absence of a meeting, a selection of the most important biological functions will be carried out. The in-depth analysis of this selection will make it possible to determine the biological significance of the results obtained (to determine if the major biological functions impacted are positively or negatively regulated and to deduce the associated consequences), to determine phenotypes, and to propose claims.


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Nano-LC-MS/MS

Nano Liquid Chromatography Coupled Mass Spectrometry - Long Gradient
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DNA Sequencing

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Metagenomics

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Transcriptomics Data Analysis

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Metabolomics

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Bioinformatics

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ELISA

Enzyme-linked immunosorbent assay
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PCR

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RT-PCR

Reverse transcription polymerase chain reaction
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qPCR

Quantitative PCR
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