SkinMet_comparison_V1V3_SRA_experiment.conf
Skin microbiome studies are increasingly common, due in part to affordable and accessible sequencing and analysis platforms. Compared to culture-based techniques, DNA sequence-based methods, such as sequencing of the bacterial 16S ribosomal RNA (rRNA) gene, provide more precise microbial community characterizations. Although outcomes of microbiome studies heavily depend on the protocols employed, skin-specific approaches have not been optimized. Here we establish a resource for the cutaneous research community to guide skin microbiome experimental design. We compare 16S rRNA gene tag sequencing to whole metagenomic shotgun (WMS) sequencing for deciphering skin microbiome community composition, diversity, and function. We show that reported relative abundance of skin microbiota depends on the region of the 16S rRNA gene that is amplified and sequenced. Primers widely used for studies of the gastrointestinal microbiome poorly recapitulate relative abundance of the skin commensal Propionibacterium. Alternatively, sequencing of hypervariable regions 1-3 provides similar genus-level classifications of bacterial communities to WMS sequencing. A perceived advantage of WMS sequencing is that it provides evidence of a community’s functional potential
16S amplicons were generated following procedures outlined by Caporaso et al. (2012). Caporaso JG, et al. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6(8): 1621-1624.