Laboratory contamination in airway microbiome studies

Autor:	Christine Drengenes, Harald G. Wiker, Tharmini Kalananthan, Eli Nordeide, Tomas M. L. Eagan, Rune Nielsen
Jazyk:	angličtina
Rok vydání:	2019
Předmět:	Microbiome Contamination Low biomass Respiratory 16S rRNA gene Microbiology QR1-502
Zdroj:	BMC Microbiology, Vol 19, Iss 1, Pp 1-13 (2019)
Druh dokumentu:	article
ISSN:	1471-2180
DOI:	10.1186/s12866-019-1560-1
Popis:	Abstract Background The low bacterial load in samples acquired from the lungs, have made studies on the airway microbiome vulnerable to contamination from bacterial DNA introduced during sampling and laboratory processing. We have examined the impact of laboratory contamination on samples collected from the lower airways by protected (through a sterile catheter) bronchoscopy and explored various in silico approaches to dealing with the contamination post-sequencing. Our analyses included quantitative PCR and targeted amplicon sequencing of the bacterial 16S rRNA gene. Results The mean bacterial load varied by sample type for the 23 study subjects (oral wash>1st fraction of protected bronchoalveolar lavage>protected specimen brush>2nd fraction of protected bronchoalveolar lavage; p
Databáze:	Directory of Open Access Journals
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