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Laboratory contamination in airway microbiome studies.


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?ConclusionsThe influence of laboratory contamination will vary across airway microbiome studies. By reporting estimates of contaminant levels and taking use of contaminant identification tools (e.g. the Decontam R package) based on statistical models that limit the subjectivity of the researcher, the accuracy of inter-study comparisons can be improved.

SUBMITTER: Drengenes C 

PROVIDER: S-EPMC6694601 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Publications

Laboratory contamination in airway microbiome studies.

Drengenes Christine C   Wiker Harald G HG   Kalananthan Tharmini T   Nordeide Eli E   Eagan Tomas M L TML   Nielsen Rune R  

BMC microbiology 20190814 1


<h4>Background</h4>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 quantita  ...[more]

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