Abstract
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 metagen-omic 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.
Original language | English |
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Article number | 001058 |
Number of pages | 14 |
Journal | Microbial Genomics |
Volume | 9 |
Issue number | 7 |
DOIs | |
Publication status | Published - 10 Jul 2023 |
Bibliographical note
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.
Publisher Copyright:
© 2023 The Authors.
Keywords
- Long and short read sequencing
- Microbial abundance
- Skin microbiome
ASJC Scopus subject areas
- Epidemiology
- Microbiology
- Molecular Biology
- Genetics