Experimental metagenomics and ribosomal profiling of the human skin microbiome

Abstract

The skin is the largest organ in the human body, and it is populated by a large diversity of microbes, most of which are co-evolved with the host and live in symbiotic harmony.There is increasing evidence that the skin microbiome plays a crucial role in the defense against pathogens, immune system training and homoeostasis, and microbiome perturbations have been associated with pathological skin conditions. Studying the skin resident microbial community is thus essential to better understand the microbiome-host crosstalk and to associate its specific configurations with cutaneous diseases. Several community profiling approaches have proved successful in unravelling the composition of the skin microbiome and overcome the limitations of cultivation-based assays, but these tools remain largely inaccessible to the clinical and medical dermatology communities. The study of the skin microbiome is also characterized by specific technical challenges, such as the low amount of microbial biomass and the extensive human DNA contamination. Here, we review the available community profiling approaches to study the skin microbiome, specifically focusing on the practical experimental and analytical tools necessary to generate and analyse skin microbiome data. We describe all the steps from the initial samples collection to the final data interpretation, with the goal of enabling clinicians and researchers who are not familiar with the microbiome field to perform skin profiling experiments. K E Y W O R D Smetagenomics, next generation sequencing, profiling, ribosomal, skin microbiome, skin microbiome, metagenomics, ribosomal profiling

Molecular detection of fungal and bacterial DNA from pustules in patients with palmoplantar pustulosis: special focus on Malassezia species

“…We found no bacterial DNA in the pustules, contrary to the report of Masuda‐Kuroki et al . We used the primer set for a full‐length sequence of the nine specific regions (V1–V9) due to the accurate taxonomic classification, whereas Masuda‐Kuroki et al . used primers specific to the V1–V2 region, which can yield a positive result.…”

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Improving saliva shotgun metagenomics by chemical host DNA depletion

“…These kits have improved microbial sequencing yield in a variety of sample types, including bronchoalveolar lavage fluid [ 8 ], blood [ 9 ], and sonicate fluid from prosthetic joint infections [ 10 ]. However, the multiple wash steps required limit the potential of low biomass samples to be successfully treated [ 11 ]. Furthermore, loss of bacterial DNA and a potential bias toward Gram-positive taxa has been reported [ 12 ].…”