ArticleBMC microbiology2019
Laboratory contamination in airway microbiome studies.
Article in BMC microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
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Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Human Respiratory Microbiome: Current Understandings and Future Directions.American journal of respiratory cell and molecular biology · 2023Pooled it
- Gut-lung axis and microbiome alterations in mycobacterial infections: from pathogenesis to therapeutic potential.Gut microbes · 2026Review
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Mitochondria Meet the Lung Microbiome: A Bidirectional Dialogue in Inflammation and Respiratory Diseases.Biomedicines · 2026Review
- Comparing saliva collection and DNA extraction methods for saliva-based microbiome profiling.Frontiers in microbiology · 2026Article
- The oral and lower airway microbiota and coronary heart disease in COPD patients and controls.PloS one · 2026Article
- Pulmonary injury in inflammatory bowel disease: intestinal barrier disruption, gut-lung axis remodeling, and treatment-related lung toxicity.Frontiers in immunology · 2026Review
- LungMicroHostR: an R package for integrated host-microbiome analysis of bronchoalveolar lavage fluid metagenomic sequencing data.Frontiers in bioinformatics · 2026Article
- Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.PloS one · 2026Article
- Progressive microbial alterations in the human gut and lung across early life: implications for translational medicine.Frontiers in cellular and infection microbiology · 2026Review
- Article
- Bacterial DNA Contamination of Commercial PCR Enzymes: Considerations for Microbiome Protocols and Analysis.Microorganisms · 2025Article
- Early-Life Host-Microbial Interactions and Asthma Development: A Lifelong Impact?Immunological reviews · 2025Review
- E-Cigarette Use, Cigarette Smoking, and Sex Are Associated With Nasal Microbiome Dysbiosis.Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco · 2024Article
- Lung microbiome on admission in critically ill patients with acute bacterial and viral pneumonia.Scientific reports · 2023Article
- Sample Collection Methods in Upper Gastrointestinal Research.Journal of Korean medical science · 2023Review
- Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling.Animal microbiome · 2023Article
- Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples.Future science OA · 2023Article
- Alterations of lower respiratory tract microbiome and short-chain fatty acids in different segments in lung cancer: a multiomics analysis.Frontiers in cellular and infection microbiology · 2023Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsThe 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 < 0.001). By comparison to a dilution series of know bacterial composition and load, an estimated 10-50% of the bacterial community profiles for lower airway samples could be traced back to contaminating bacterial DNA introduced from the laboratory. We determined the main source of laboratory contaminants to be the DNA extraction kit (FastDNA Spin Kit). The removal of contaminants identified using tools within the Decontam R package appeared to provide a balance between keeping and removing taxa found in both negative controls and study samples.
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.
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