UMI-guided single locus sequence typing method for phylotyping Cutibacterium acnes from skin samples

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Cutibacterium acnes is a key skin bacterium with diverse strains impacting skin health.
• Characterizing C. acnes strains in skin samples is difficult due to low DNA amounts and contamination.

Purpose of the Study:

• To introduce SLST-Seq, a novel method for high-resolution C. acnes strain typing from low-input skin samples.
• To enable accurate, culture-independent analysis of C. acnes population structure in situ.

Main Methods:

• SLST-Seq utilizes single-locus sequence typing (SLST) with synthetic long-read sequencing.
• Combines unique molecular identifier barcoding and de novo assembly for full-length SLST reconstruction.
• Validated using controls, dilution series, and reproducibility assessments.

Main Results:

• SLST-Seq demonstrated high specificity, quantitative accuracy, and reproducibility.
• Analysis of skin-strip samples revealed significant inter-individual variability in C. acnes communities.
• Skin microbiome structures were largely consistent between facial and back sites within individuals.

Conclusions:

• SLST-Seq offers a sensitive and scalable framework for analyzing C. acnes population dynamics.
• This method facilitates high-resolution studies of skin microbiome composition in challenging samples.