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Laboratory contamination over time during low-biomass sample analysis.
Weyrich, Laura S; Farrer, Andrew G; Eisenhofer, Raphael; Arriola, Luis A; Young, Jennifer; Selway, Caitlin A; Handsley-Davis, Matilda; Adler, Christina J; Breen, James; Cooper, Alan.
Afiliación
  • Weyrich LS; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.
  • Farrer AG; ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia.
  • Eisenhofer R; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.
  • Arriola LA; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.
  • Young J; ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia.
  • Selway CA; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.
  • Handsley-Davis M; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.
  • Adler CJ; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.
  • Breen J; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.
  • Cooper A; ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia.
Mol Ecol Resour ; 19(4): 982-996, 2019 Jul.
Article en En | MEDLINE | ID: mdl-30887686
Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Errores Diagnósticos / Metagenómica / Contaminación de ADN / Biología Molecular Tipo de estudio: Diagnostic_studies Idioma: En Revista: Mol Ecol Resour Año: 2019 Tipo del documento: Article País de afiliación: Australia Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Errores Diagnósticos / Metagenómica / Contaminación de ADN / Biología Molecular Tipo de estudio: Diagnostic_studies Idioma: En Revista: Mol Ecol Resour Año: 2019 Tipo del documento: Article País de afiliación: Australia Pais de publicación: Reino Unido