Isolation and Identification of the Follicular Microbiome: Implications for Acne Research

Abstract

Our understanding of the microbiome and the role of Propionibacterium acnes in skin homeostasis and acne pathogenesis is evolving. Multiple methods for sampling and identifying the skin's microbiome exist, and understanding the differences between the abilities of various methods to characterize the microbial landscape is warranted. This study compared the microbial diversity of samples obtained from the cheeks of 20 volunteers, collected by surface swab, pore strips, and cyanoacrylate glue follicular biopsy, all sequenced with 16S rRNA sequencing (V1-V3) and whole-genome metagenomic sequencing. The sequencing method of choice influenced the detection of microbial profiles as whole-genome sequencing captured more species diversity, including viruses, compared with 16S sequencing. The relative abundance of bacterial or fungal species and overall diversity did not differ between sampling methods. However, the viral composition of the skin's surface is unique compared with the follicle, suggesting distinct viral niches within the skin. P. acnes bacteria, ribotypes, and bacteriophages were identified equally by all sampling methods indicating that the sampling method, whether for the skin's surface or follicle, does not impact P. acnes-related characterization and that all may be equally useful for acne-related research studies.

The role of the skin microbiota in acne pathophysiology

“…78 A recent study compared sampling using surface swabs, pore strips and cyanoacrylate glue follicular biopsy. 79 While differences exist, overall, the relative abundance of bacterial and fungal species and the taxonomic diversity detected were similar. However, the viral composition was different on the surface and in the follicle.…”

“…The pore strip and cyanoacrylate biopsy have the advantages of being noninvasive, capturing the upper stratum, and isolating the pilosebaceous unit via dissection, thereby minimizing the potential for surface contamination . A recent study compared sampling using surface swabs, pore strips and cyanoacrylate glue follicular biopsy . While differences exist, overall, the relative abundance of bacterial and fungal species and the taxonomic diversity detected were similar.…”

Skin microbiota: Friend or foe in pediatric skin health and skin disease

“…There is no “gold standard” for sampling method, which should be tailored to the study question. Published studies comparing multiple methods in the same individual show each method isolates similar populations, but not 100% identical populations . In children, the most utilized method is the non‐invasive swab which samples the skin's surface and upper portion of the hair follicles (Figure A).…”

“…Identification of sampled microbes has been accelerated by next‐generation sequencing technologies, including 16S ribosomal RNA (rRNA) gene sequencing (bacteria), internal transcribed‐spacer sequencing (ITS1 or ITS2; fungi), or whole‐genome shotgun sequencing (WGS; bacteria, fungi, and viruses) (Figure B). However, just like sampling methods, sequencing methods do not yield identical results and caution is advised when comparing data sets with different methods . WGS could be considered the “gold standard” as it provides information about all taxonomic kingdoms; however, it is also the most costly option.…”

“…However, just like sampling methods, sequencing methods do not yield identical results and caution is advised when comparing data sets with different methods. 10,12,13 WGS could be considered the "gold standard"…”