When it is to Understand What is Really Going on by Phylogene

16 February 2023

In the last years, a lot of study were made with metagenomics which allowed to have information on the taxonomic composition of microbiomes with 16SrDNA (1) or information on the metabolic pathways possibilities with WGS (2).

With these techniques, we were able interestingly to answer to a question like : « Does my product impact the balance of the microbiome? », or « Is my product microbiome friendly ? » particularly with skin ingredients, but we were staying frustrated when something was moving between two conditions, because none of these techniques could answer to the questions: « What are the microbes doing ? » or « Taxons composition is moving, is it good or bad ? » (3)

Now, the tendancy is to couple metagenomic research with other omics in order to paint a much more comprehensive and detailed picture of what is occurring between the host and skin microbes in healthy and diseased states.(3)

Anyway, in the frame of known microbiome genes, looking at the omics to be coupled :

Metatranscriptomics remains linked to potential events (3) and indicates that something may occur.

Metabolomics which cumulates the cost of 3 different techniques remains highly limited by the fact that the majority of gut microbiome-derived small molecules (>90%) do not have any references in public databases despite their immediate relevance to host physiology. (5) (7)

Metaproteomics remains able to reach host and microbiome real active functions then host-microbiome interactions (6) at costs which are similar to those of metagenomics or metatranscriptomics experiments (4), can provide same taxonomic informations based on proteins (6). Based on untargeted relative quantification between conditions, it is the ideal tool to understand what really occurs between samples.

(1) Meisel JS, Hannigan GD, Tyldsley AS, et al. Skin Microbiome Surveys Are Strongly Influenced by Experimental Design. J Invest Dermatol. 2016;136:947-56..

(2) Ranjan R, Rani A, Metwally A, et al. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun. 2016;469:967-77.

(3) 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.Sandhu SS and all.. 2019 Dermatology on line journal Volume 25 Number 7| July 2019| 25(7):1

(4) Salvato F, Hettich RL, Kleiner M (2021) Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes. PLoS Pathog 17(2):e1009245.

(5) De Saedeleer, B., Malabirade, A., Ramiro-Garcia, J. et al. Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics. ISME COMMUN. 1, 82 (2021).

(6) Oleg Karaduta, Zeljko Dvanajscak,and Boris Zybailov

Metaproteomics—An Advantageous Option in Studies of Host-Microbiota Interaction. Microorganisms. 2021 May; 9(5): 980.

(7) Jody C. May and John A. McLean Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12; 9(1): 387–409.

With PHYLOGENE, you can characterize and understand the effects as well.

Specific targeted PCR for dedicated genus/species,

Bacterial 16s rDNA and fungal ITS sequencing with OTU-based estimation to investigate microbial communities diversity and determine taxonomic composition,

High-resolution nano LC-MS/MS quantitative metaproteomics and HolXplore™ data processing: The efficient tool for functional understanding.