The Challenge of Accurately Performing Skin Microbiome Metagenomic Studies

Posted 27th November 2017 by Jane Williams

The human skin is densely colonised with a complex microbial community ⁽¹⁾. Microbes are a part of the skin barrier that, combined with  innate immunity, keeps the balance essential to maintaining healthy skin ⁽²⁾. Recent and independent research projects strongly suggested that human skin microbiota is of a major importance for human health and could be targeted to improve the skin health.

It is generally believed that a healthy skin microbiota is characterised by a considerable diversity of commensal or even beneficial (symbiotic) bacteria ⁽³⁾. Many human skin disorders and diseases have been linked with changes in the skin microbiota composition and/or functionality. In acne vulgaris patients the population structure on the strain level of Propionibacterium acnes was different ⁽⁴⁾, Psoriasis patients are characterised by increase in the abundance of the major skin genera resulting in a community differentiation of the cutaneous microbiota of psoriatic patient ⁽⁵⁾. Atopic dermatitis and seborrhoeic dermatitis are linked to an increase in Staphylococcus aureus levels and to the fungi Malassezia levels respectively. However, it still unknown in most cases whether these changes in the microbiome are the cause or the consequences of the pathology.

Consequently, in order to better understand this relationship between the skin microbiome and the skin health, the number of metagenomic studies on skin microbiome has exploded in the last decade and nowadays due to affordable and unexpensive DNA sequencing technologies. Nevertheless, study design for skin microbiome research is multifaceted and integral to all downstream steps. Many published studies examined the biases introduced by the skin sampling methods ^{(6, 7)} and sample storage ⁽⁸⁾, controls and contamination sources ⁽⁹⁾, sequencing biases ⁽¹⁰⁾, and possible quantitation ⁽¹¹⁾. The complexity of skin microbiome studies is nicely summarised in the title of the review from ⁽¹²⁾ “Performing Skin Microbiome Research: A Method to the Madness”.

Standardisation and validation of the protocols, bioinformatic pipelines and sequencing platforms is a crucial step for a successful skin microbiome analysis. This validation and harmonisation approach is of crucial importance for L’Oréal Research and Innovation where it has developed a complete validation process for our international sequencing platforms CROs and harmonised the methods used for skin microbiome studies.

Ahmad Khodr is a Researcher at the International Microbiology Department of L’Oréal Research & Development. Ahmad will be presenting in the NGS Tech and Applications Strand of next month’s 4Bio Summit.

View the 4Bio Summit agenda to find out more about Ahmad’s presentation.

Tags: metagenomics, microbiome, microbiota, next generation sequencing, next-gen sequencing, NGS, plant genomics, sequencing, skin