A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin
JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift)
 
ID 2206457
Author(s) Garcia-Garcerà, Marc; Garcia-Etxebarria, Koldo; Coscollà, Mireia; Latorre, Amparo; Calafell, Francesca
Author(s) at UniBasel Coscollá Devís, Mireia
Year 2013
Title A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin
Journal PLoS ONE
Volume 8
Number 9
Abstract In the last decade, an extensive effort has been made to characterize the human microbiota, due to its clinical and economic interests. However, a metagenomic approach to the skin microbiota is hampered by the high proportion of host DNA that is recovered. In contrast with the burgeoning field of gut metagenomics, skin metagenomics has been hindered by the absence of an efficient method to avoid sequencing the host DNA. We present here a method for recovering microbial DNA from skin samples, based on a combination of molecular techniques. We have applied this method to mouse skin, and have validated it by standard, quantitative PCR and amplicon sequencing of 16S rRNA. The taxonomic diversity recovered was not altered by this new method, as proved by comparing the phylogenetic structure revealed by 16S rRNA sequencing in untreated vs. treated samples. As proof of concept, we also present the first two mouse skin metagenomes, which allowed discovering new taxa (not only prokaryotes but also viruses and eukaryots) not reachable by 16S rRNA sequencing, as well as to characterize the skin microbiome functional landscape. Our method paves the way for the development of skin metagenomics, which will allow a much deeper knowledge of the skin microbiome and its relationship with the host, both in a healthy state and in relation to disease.
Publisher Public Library of Science
ISSN/ISBN 1932-6203
edoc-URL http://edoc.unibas.ch/dok/A6184015
Full Text on edoc Available
Digital Object Identifier DOI 10.1371/journal.pone.0074914
PubMed ID http://www.ncbi.nlm.nih.gov/pubmed/24073227
ISI-Number WOS:000324768000036
Document type (ISI) Article
 
   

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11/08/2020