An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs

Serghiou, Iliana R., Baker, Dave, Evans, Rhiannon, Dalby, Matthew J., Kiu, Raymond, Trampari, Eleftheria, Phillips, Sarah, Watt, Rachel, Atkinson, Thomas, Murphy, Barry, Hall, Lindsay J. ORCID: and Webber, Mark A. (2023) An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs. Microbial Genomics, 9 (7). ISSN 2057-5858

[thumbnail of mgen001058]
PDF (mgen001058) - Published Version
Available under License Creative Commons Attribution.

Download (5MB) | Preview


The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.

Item Type: Article
Additional Information: Funding Information: This research was supported in part by the NBI Computing infrastructure for Science (CiS) group through the provision of a High-Performance Computing (HPC) Cluster. I.R.S. is funded by a Biotechnology and Biological Sciences Research Council (BBSRC) CTP studentship with Unilever (BB/T508974/1). L.J.H. is supported by Wellcome Trust Investigator Awards 100974/C/13/Z and 220876/Z/20/Z; and a BBSRC Institute Strategic Programme, Gut Microbes and Health BB/R012490/1, and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. M.A.W. is supported by project grant (BB/T014644/1) from the Biotechnology and Biological Sciences Research Council and BBSRC Institute Strategic Programmes Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10349.
Uncontrolled Keywords: long and short read sequencing,microbial abundance,skin microbiome,genetics,molecular biology,epidemiology,microbiology,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1300/1311
Faculty \ School: Faculty of Science > School of Biological Sciences
Faculty of Science
Faculty of Medicine and Health Sciences > Norwich Medical School
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 01 Aug 2023 12:31
Last Modified: 08 Aug 2023 08:30
DOI: 10.1099/mgen.0.001058


Downloads per month over past year

Actions (login required)

View Item View Item