Laboratory contamination over time during low-biomass sample analysis

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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 five years to characterize long-term contaminant
diversity. We additionally compared the contaminant content within a homemade silica-based
extraction method, commonly used to analyse low-endogenous samples, with a widely
used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean
ancient DNA laboratory was unique compared to the modern molecular biology laboratories,
and changed over time according to researchers, month, and season. The commercial
kit contained higher microbial diversity and several human-associated taxa in
comparison to the homemade silica extraction protocol. We recommend a minimum
of two strategies to reduce the impacts of laboratory contaminants within low-biomass
metagenomic studies: 1) extraction blank controls should be included and sequenced
with every batch of extractions and 2) the contributions of laboratory contamination
should be assessed and reported in each high-throughput metagenomic study.