Phylogene news

It is now well known that microorganisms present at the skin surface are in perfect symbiosis with the skin. We can even say now that skin is made of a human and a microbial part, this is the concept of the holobiont (2). Anyway microbes are the first range of protection against external aggression causing skin aging.

Metaproteomics is able to reach in an untargeted way both human and microbial proteins together, coupled with bioinformatics and AI data processing. Based on a relative quantification of proteins between conditions made by nanoLC-MS/MS, it allows to more precisely understand what are the mechanisms involved in effects.(3) (4)

Our publication with partners (1) shows by comparison of young and aged dehydrated skins and in protection or restoration by a powerful ingredient at the taxonomic and biological functional levels .

https://www.mdpi.com/2079-9284/11/4/132

As kinetics and level of expression of omics are different, the multi-omics tendancy is to couple different omics in order to paint a much more comprehensive and detailed picture of what is occurring between the host and microbes in healthy and diseased states(1).

Recently, new studies on skin used metagenomics coupled to metabolomics (2) (4). Of course metabolomics is attractive as being the final stage of the metabolization of substrates and reaching the molecular forms of exchanges within the microbiota and with the host. Even if limitations like only 10% of microbial and human metabolites being identified in the databases (5), it remains interesting to know more about for example fatty acids which are the most important components in maintaining the skin barrier function or lactic acid which is a key component of the skin’s natural moisturizing factor and keeps skin hydrated (4), or lipids as key components of the skin (3).

Then, it is logical to couple the omics which are in charge of the functions and which detect the production of the functions, namely metaproteomics and metabolomics(6), which will better track the host-microbes interactions (2), as metaproteomics reaches simultaneously the proteins of the skin and its microbiota which produce the metabolites to be detected. It is particularly efficient as it is often seen that there is no change at skin microbial abundance, taxonomic or functional metagenomics level but shifts appear at the real functional and metabolic levels , as discussed by these authors.(4)

PHYLOGENE is familiar in using the complementarity between metagenomics and metaproteomics to obtain more focused claims .

Now based on its expertise in metaproteomics, PHYLOGENE is completing its proposed services as close as possible to real functionality with metabolomics dedicated to skin metabolism . This metaproteomics and metabolomics toolset makes it possible to generate knowledge of the effects of skin diseases or the mechanisms of action of cosmetics, prebiotics, probiotics or drugs targeting the skin microbiome.

Metaproteomics:

Proteins are in charge of cellular structures and functions of life activities. Proteomics provides insights into the composition and activity patterns of intracellular proteins and protein-protein interactions.

Metaproteomics makes it possible to achieve simultaneously the identification of the microbiome members, and a snapshot of the functions of the host and its microbiomes. The non-targeted approach gives the identification and relative quantification of the host and its microbiome proteins impacted by the studied phenomenon and produces a set of data reflecting the studied effect.

Metabolomics :

Metabolites are the molecules produced by the functional proteome in response to environmental stimuli. Metabolomics is the final stage of the metabolization of substrates and identifies the molecular forms of exchanges within the microbiota and with the host. The proposed approach is a targeted approach of relative quantification metabolites known for their role in the skin metabolism.

Multiomics :

With coupled metaproteomics and metabolomics, we use the potential of the two omics closest to the phenotype.

Our bioinformatics tools enable integrated and standardized proteomic and metabolomic analysis of global proteome and metabolome data. Enrichment of metabolic pathways and correlation analysis of regulatory mechanisms of upstream protein actors of metabolism and downstream metabolite changes provide a comprehensive view of the effects generated at the gut level.

 (1) Simran S Sandhu, Aunna Pourang, Raja K Sivamani. A review of next generation sequencing technologies used in the evaluation of the skin microbiome: what a time to be alive. 2019 Dermatology on line journal  Volume 25 Number 7| July 2019| 25(7):1  

(2) Jacques C and all. Multi-omics approach to understand the impact of sun exposure on an in vitro skin ecosystem and evaluate a new broad-spectrum sunscreen.

Photochem Photobiol. 2023 Jul 24. ;00 :1-14

(3) Patra V and all. Ultraviolet exposure regulates skin metabolome based on the microbiome. Sci Rep. 2023; 13: 7207.

(4) Li M and all. Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome. Front Med (Lausanne). 2023; 10: 1165980.

(5) Peisl BYL and all. Dark matter in host-microbiome metabolomics: Tackling the unknowns–A review. Analytica Chimica Acta Volume 1037, 11 December 2018, Pages 13-27

(6) Oleg Karaduta, Zeljko Dvanajscak,and Boris Zybailov. Metaproteomics—An Advantageous Option in Studies of Host-Microbiota Interaction. Microorganisms. 2021 May; 9(5): 980.

  PHYLOGENE to talk about omics technos for microbiome products effects substantiation

PHYLOGENE team proud to be awarded as best poster at Targeting Microbiota 2022.

Get your skin biopsies kit in your lab from CTIBiotech, apply your product, send the biopsies to Phylogene for proteomics analysis, receive your results from CTIBiotech and Phylogene

Our poster with partners at SID 2022 about the effects of an ingredient evaluated by metaproteomics and dedicated bioinformatics.

DeepMicro: A project where Phylogene and the CEA will develop metaproteomics for understanding microbiomes

     Bioinformatician biologist

PHYLOGENE will be at IN-COSMETICS GLOBAL next April. Visit our stand P84 to see our innovations or don't hesitate to make an appointment, we will be even more available to discuss your past and future projects and find out if we can be of use to you.

Publication with partners on lipid metabolism in different types of skins exposed to sun using LC-MS/MS proteomics and lipidomics

We perfected sample preparations for the proteomic analysis of strip samples in dermo-cosmetics which now only requires a single strip to reach an even higher number of proteins

Host cell proteins can be now quantified in a untargeted way instead of using only some classic proteins by ELISA

Exploring the Emerging Role of the Gut Microbiota and Tumor Microenvironment in Cancer Immunotherapy

Our new publication which shows how LC-MS/MS proteomics can reveal in an untargeted way the modifications of the intracellular fibroblast collagen proteome induced by differential treatments.

How to characterize microbiota metabolism on scalp

Our publication in Cosmeticobs about modes of action on skin and its microbiota using omics techniques

PHYLOGENE will attend BIO Digital June 10-11 & 14-18, 2021 and One-on-One Partnering.
We would be pleased to share some time with you to talk about your projects on which we could be useful.

Phylogene is proud to be part of the "Alliance Promotion Microbiote”.

This initiative should gather major microbiome industry actors in efforts to put the microbiome at the heart of diagnostic and therapeutic strategies for better care.

Thank you for the time spent with us at BIOFIT 2020, Oncology virtual partnering meeting 2021, NUTREVENT 2021, we look forward to seeing you again next edition!

A new publication in hematology based on plasma samples analysed by nanoLC-MS/MS proteomics method of choice for biomarker generating

Our proteomics and bioinformatics study with partners contributed to understand the structure and working of the new human innervated reconstituted epidermis in testing ingredients effects

We look forward to talking to you about omics and bioinformatics for active molecules, pharmabiotics, diets or nutritional ingredients mechanisms of action and discovery on microbiotas. See an example of our tools presented in our poster.

http://www.global-engage.com/event/microbiota/#agenda

Our metagenomics publication on C acnes phylotypes

Metaproteomics allows accessing to activated functions at the human, bacteria and fungi level, metagenomics does not. To have an idea, see the link

How to get a large view on the effects of a diet on a microbiota at functional and mode of action levels

Genomics, transcriptomics, proteomics and metabolomics possibilities for cosmetics substantiation.

Our new publication in skin aging with partners

Untargeted approach, the best way for microbiota mode of action understanding.

Protein phosphorylation is a crucial mechanism in many cellular regulations and strongly involved in virtually all physiological and pathological processes such as signal transduction, cell proliferation, differentiation, apoptosis or metabolism. Signaling processes involving phosphorylation are often deregulated during pathology or stress.

METAPROTEOMICS OF OUR MICROBIOME: The evolution of LC-MS/MS allows the  investigation of proteins in our saliva or skin or gut microbiome

COSMETOLOGY : A new study in mice on UVB effects on mouse skin. Our experience is different on human skin therefore it remains important to stay in untargeted mode to be sure to keep the whole effects on pathways rather than defining variable biomarkers.

COSMETOLOGY: Substantiation tests by  comparison of proteome of fibroblasts, keratinocytes, skin explants, rebuilt skin, D-squame, skin swabs, extra-cellular matrix.. Please contact us for these services.

PHYLOGENE-mass spectrometry has been granted by EUROSTARS for its NOSO-FIGHT project about Healthcare-Associated Infections.

PHYLOGENE-mass spectrometry is involved to the ID-THON project about tuna species identification

PHYLOGENE-mass spectrometry is partner of KINDReD, a FP7-Health-2013 Innovation project. The project is a 36 months and 14 partners project. Project aim is to develop drug candidate against kinetoplastids. PHYLOGENE- mass spectrometry is WP leader for drug's target determination.

PHYLOGENE will attend EIC 2013 on September 25th and 26th in Montpellier

XXIXth JED 2019 in Lyon Jan 31 - Feb 1st Presentation of our substantiation tools

HolXplore: A new data processing module for host+microbiota outputs of omics comparison studies.

Functional microbiome: How to understand the interactions between host and microbiota through functions .

SKIN MICROBIOME: Metagenomics and proteomics to characterize products effects

DIABETES: Understanding the diabetic nephropathy by label-free LC-MS/MS.

RedOxMics: Evaluation of the abiotic stress of the skin and oxidation deepness.

Toxicity: Untargeted proteomics allows discovering positive effects and negative effects as well.

Post translational modifications: PTMs, an essential mechanism of protein functionality

STRESS RESISTANCE AND CROP PRODUCTIVITY: A review on advances in plant proteomics. Many LC-MS//MS proteomics tools are now efficient, also available at MS-PHYLOGENE

LC-MS/MS MRM METHOD or ELISA? Do you know a multiplex LC-MS/MS MRM method can interestingly replace 20 ELISA methods at the development cost of 1 ELISA method?

Phylogene will be at Bio-Spring Europe in Paris , March 19-21, 2015

Nutrition: Studying the effects of a diet on muscle metabolism

Microbiome: Example with our tools of proteomics able to track simultaneously effects on host and microbiome

Probiotics: Multi-omics for probiotics studies and metaproteomics for mechanisms of action understanding.

Fermentation: Understanding the yeast or bacteria fermentation process with LC-MS/MS proteomics

OPHTALMOLOGY: A study showed in 2011 the interest of tears to find biomarkers by LC/MS/MS for glaucoma; This new study shows that serum contains interesting proteins as biomarkers for uveitis which were found by label-free nanLC-MS/MS and which can be followed by MRM methods

RESISTANCE TO ANTIBIOTICS:       MS-PHYLOGENE is now using its PROTABIORES database to characterize antibiotic resistance mechanisms. This LC-MS/MS peptide and protein database contains 53000 entries in September 2015

Plant metabolism: Proteomics and phosphoproteomics to study the effects of environment.

Probiotics: Proteomics and bioinformatics to understand the interactions between Lactobacilli and their environment.

Plant metaproteomics: Functional stability while taxonomic strong variability on phyllosphere.

Cancer: Proteomics in early-phase drug development and clinical trials for new biomarkers

COSMETOLOGY NEWS: UV effects, skin disorders through fibroblasts proteomes, skin microbiome by Highres proteomics.

WOUND HEALING AND TISSUE REGENERATION: Proteins of interest by label-free LC-MS/MS

CORAVALID performs a complementary analysis of identification and quantification data through a series of statistics tests. It allows exploiting all the wealth of your LC-MS/MS data.

Substantiation: An efficient innovative method

Understanding antimicrobial peptides mode of action: The ectodermal dysplasia skin secretome comparison vs controls by nanoLC-MS/MS proteomics gives a more complete understanding of the pathology

DERMATOLOGY AND BIOMARKERS: A study starting with untargetd relative quantification of psoriatic skins proteins to get a first set of 47 moving proteins followed by MRM targeted method of these proteins. Then 8 proteins were selected for further validation. A kind of routine?

FFPE and CANCER: NanoLC-MS/MS proteomics uses small parts of available slices to produce biomarkers or find targets

Interactions between microbiome and host: metaproteomics is the tool able to see both simultaneously

Publication: Prediction of the effects of an ingredient using our proteomics and bioinformatics approach.

Therapeutic antibodies: Host Cell Proteins (HCP) characterization by nanoLC-MS/MS

Publication: Photodamage on stratum corneum investigated with proteomics

PLANT IMPROVEMENT: Proteomics and metabolomics are now mature

LC-MS/MS proteomics approach of Alzheimer disesase.

COSMETOLOGY: Oxidations follow-up by UVs

Analytical alternatives for allergen detection

ALLERGENS IN WINE: Regulation n°CE 579/2012

The regulation n° 579/2012 was published on June 30th 2012. The labelling of milk or egg is now mandatory on 2012 wines when using these fining agents. Its "whereas" n° (3) goes to the OIV-COMEX 502-2012 resolution which gives the 0,25ppm detection threshold. It means that the labelling is not necessary under this detected quantity .

PHYLOGENE - allergen specialized lab- tested all the available techniques for allergen tracking in wines. Many differences were seen between the ELISA kits about the false positive and false negative results (see study). To discard these risks and secure the bottle labelling it is necessary to check these two points when starting the analysis.

Probiotics, process strains by RT-PCR

Since January 2013, PHYLOGENE is accreditated by COFRAC in flexible scope, according to  ISO 17025 standard, for allergens detection and quantification in food matrices by immunoenzymatic methods (ELISA) Ref Accreditation n°1-2128-testing- Scope available on www.cofrac.fr

Yes, PHYLOGENE realizes for 13 years species identification, terrestrial and fishes

Yes, this is targeted detection, the choice of species depends on your estimated risk.

Yes, the quantification is possible. It is of the type: horse/horse+beef

Metagenomics recent developments now enable the skin microbiome investigation. PHYLOGENE offers bacterial 16s rDNA and fungal ITS sequencing with OTU-based approaches to investigate microbial communities diversity and determine taxonomic composition for cosmetics evaluation

(see also LC-MS/MS proteomics for metaproteomics)

Cosmetic 360 in Paris: A lot of interest of our combined genomic and proteomic approach of skin and microbiome.

CANCER: A study of phosphoproteins and signaling networks in bioological cell lines and tissues allows understanding induced effects by cancer and also drug resistance

CORAVALID

LC-MS/MS output data are rich but often large and complex to be treated. So it takes a lot of time to our customers.

STEM CELLS: Mechanisms and biomarkers of differentiation by HR proteomics.

BIOMARKER AND DISCOVERY WORKFLOW: our poster at EBF 2015

RESISTANCE TO ANTIBIOTICS: Impact of rapid diagnostics on antibiotic misuse.

Our posters at IFSCC2018: "Hypothesis free" proteomics and its dedicated bioinformatics efficient for studying the corneome and ceramidome of photodamaged SC, the secretome of fibroblasts, and effects of Prunus enzymatic extracts on skin explants.

Phylogene and Dermatec collaboration on skin microbiome:
Based on its well established cohorts of volunteers and its qualified teams, Dermatec designs and realizes clinical trials in dermo-cosmetics with necessary specific biological samples dedicated to skin microbiome study.
On these samples, Phylogene does genomics and/or proteomics testing and associated bioinformatics /biostatistics data processing which highlight the effects on skin and its microbiome.
A good solution for your microbiome studies!

CRISPR-Cas9 modifications checking: LC-MS/MS proteomics is a good tool for specific and unspecific modifications as well.

Leaf heterosis in label-free proteomics.

CANCEROLOGY: Kinome and kinases inhibitors by LC-MS/MS. Please contact us for these evaluations.

INFECTIOUS DISEASES: The infectious process of Dengue virus followed by HighRes proteomics. Please contact us for these tests.

JOURNEES JP MARTY: PEAU ET MICRORGANISMES 8-9 Dec 2015. This nice meeting updated us on skin microbiome

SID 2016 (Society for Investigative Dermatology): Our poster on the UVs effects on stratum corneum determined by highres quantitative LC-MS/MS proteomics

AIS 2017: ADCs event: our poster

Our poster at ESDR2017: The possibilities of proteomics to study skin and its microbiome simultaneously at the functional level.

VACCINES: The Outer Membrane Vesicles as a source of vaccine antigens.

CANCEROLOGY: An example of biopsy comparison.

New nanoLC-MS/MS: MS Phylogene received this end of 2016 a nanoLC U3000 Dionex coupled to a Q-Exactive PLUS HCD Thermo for the best performances in proteomics and metabolomics.

Synergy meeting in Modena on Drug Development for Neglected Parasitic Diseases FP7 funded projects where Kindred project is one of the 4 projects: Our poster on kinases and kinases inhibition profiling.

IFSCC 2016: Our poster on MS proteomics of dry  skin in different ethnic groups has been awarded as one of the top 10 out of 313. It shows the power of the method in revealing new involved pathways.

The comparison of Bifidobacterium strains by label-free LC-MS/MS allows their differentiation in the process.

During Cosmetic days 2014 meeting, PHYLOGENE presented a poster: "High-resolution nano LC-MS/MS proteomics and CORAVALID data processing: For a new approach of substantiation tests "