Bio-Me’s fast, cost-effective platform generates an accurate and quantitative picture of the skin microbiome

5 January 2024

Bio-Me is a service provider, operating B2B and B2B2C, to help our clients analyze their skin and beauty products by profiling the skin microbiome.  Our qPCR-based Precision Microbiome Profiling (PMP™) platform is fast, high-throughput, cost-effective and it provides very high resolution (species/subspecies level).  Furthermore, our method is not impacted by host DNA and we provide absolute quantification for each organism, with data in a simple format.

The skin naturally houses a community of microorganisms including bacteria, fungi, viruses, archaea, and mites, that are collectively referred to as the skin microbiota. The microbiota, when considered together with their structural and genomic elements within the skin environmental niche, are referred to, in totality, as the skin microbiome1,2.  The skin microbiome is linked with many processes that are important for human health including (but not limited to) immunity, cutaneous barrier function, UV response, cutaneous repair and skin ageing2.  As a result, there is growing recognition of the value in examining how beauty and cosmetic products impact the skin microbiome.

Historically, skin microbiome profiling has been performed via 16S rRNA gene sequencing, but this provides only low resolution (usually limited to the genus level).  Whole genome sequencing via shotgun metagenomics provides excellent resolution but it is complicated by the fact that host DNA (which can occupy over 90% of a skin sample) will also be sequenced. To obtain sufficient coverage of the actual microbes, high-depth sequencing must therefore be performed, which is costly3,4.

At Bio-Me, our Precision Microbiome Profiling platform (PMP™), which involves a high-throughput qPCR system with a unique assay design/validation pipeline, successfully overcomes these challenges.  We have created over 50 specific assays, targeting the most relevant skin bacteria and fungi, to deliver a comprehensive picture of the skin microbiome at a glance.

Bio-Me’s PMP™ platform achieves very high resolution (species/subspecies level), which is superior to the resolution obtained via 16S rRNA gene sequencing. Cutibacterium acnes (C. acnes) exemplifies the importance of subspecies interrogation, because specific C. acnes phylotypes are differentially associated with diseased (acne vulgaris) or healthy skin5. Another key feature of our qPCR-based approach is that it is not impacted by host DNA (in contrast to shotgun metagenomics). In addition, we deliver absolute quantification (we state the number of genomes per taxa). The PMP™ platform is high-throughput and generates results quickly; for example, we can run 192 samples and analyze 54 targets for each, and it takes just 2-5 hours in the lab.  Our data are reported in a simple format – no need for bioinformatics for data processing!

Central to our PMP™ platform is our unique qPCR assay pipeline whereby each microbial target is thoroughly researched for prevalence, abundance and physiological relevance, and the assays are then designed with scrupulous validations in silico and in the wet lab.  This careful process culminated in the creation of the Comprehensive Skin Microbiome panel, which detects a repertoire (50+) of the most important skin microbes to rapidly deliver an accurate, quantitative, and comprehensive picture of the skin microbiome.  We can even create and validate custom strain assays, enabling clients to, for example, track engraftment of a proprietary probiotic against the background of normal skin microflora! In addition, we offer an extensive gut panel (with over 100 bacterial species), for interrogation of the gut microbiome. This can be useful to gain insight into the ‘gut-skin axis‘, which involves a clear link between the gut microbiome and skin homeostasis5.

 

To find out more please visit: https://bio-me.com/skin-microbiome-profiling/

Bio-Me

Oslo Science Park

Gaustadalléen 21

N-0349 Oslo

NORWAY

e-mail: info@bio-me.com

www.bio-me.com

 

References

  1. Berg, G. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020).
  2. Smythe, P. & Wilkinson, H. N. The Skin Microbiome: Current Landscape and Future Opportunities. Int. J. Mol. Sci. 24(4) 3950 (2023).
  3. Liu, Y. X. et al. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell 12, 315–330 (2021).
  4. Ruuskanen, M. O. et al. Towards standardized and reproducible research in skin microbiomes. Environ. Microbiol. 24, 3840–3860 (2022).
  5. Sánchez-Pellicer, P., et al. Acne, Microbiome, and Probiotics: The Gut–Skin Axis. Microorganisms Jul; 10(7): 1303 (2022).

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