Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes

• Published in: BMC microbiology Vol. 19; no. 1; p. 214
• Main Authors: Verbanic, Samuel, Kim, Colin Y, Deacon, John M, Chen, Irene A
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 05.09.2019; BioMed Central; BMC
• Subjects: Bacterial genetics; Bacteriophage; Biomass; Deoxyribonucleic acid; DNA; DNA purification; Genomes; Information management; Methodology; Microbiomes; Microbiota (Symbiotic organisms); Microorganisms; Optimization; Phages; Polymerase chain reaction; RNA sequencing; Sample preparation; Skin; Skin microbiome; Wounds; Bacteriophage; Skin microbiome; DNA purification
• ISSN: 1471-2180; 1471-2180
• DOI: 10.1186/s12866-019-1586-4

Characterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic. We find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method. Use of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples.