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New perspectives on microbial community distortion after whole-genome amplification
Citation:
Probst, A. J., T. Weinmaier, T. Z. DeSantis, J. W. Santo-Domingo, AND N. Ashbolt. New perspectives on microbial community distortion after whole-genome amplification. PLOS ONE . Public Library of Science, San Francisco, CA, 10(5):e0124158 (16 p), (2015).
Impact/Purpose:
In order to process microbial samples of low biomass using molecular techniques, it is necessary to amplify the nucleic acid pool using techniques such as whole genome amplification (WGA). The biases assocaited with this step are not well characterized for environmental samples. In this study, we used phylogenetic microarrays to determine the potential artificats introduced by WGA and this may impact analysis of microbial community composition.
Description:
Whole-genome amplification (WGA) has become an important tool to explore the genomic information of microorganisms in an environmental sample with limited biomass, however potential selective biases during the amplification processes are poorly understood. Here, we describe the effects of WGA on 31 different microbial communities from five biotopes that also included low-biomass samples from drinking water and groundwater. Our findings provide evidence that microbiome segregation by biotope was possible despite WGA treatment. Nevertheless, samples from different biotopes revealed different levels of distortion, with genomic GC content significantly correlated with WGA perturbation. Certain phylogenetic clades revealed a homogenous trend across various sample types, for instance Alpha- and Beta-Proteobacteria showed a decrease in their abundance after WGA treatment. On the other hand, Enterobacteriaceae, an important biomarker group for fecal contamination, were strongly affected by WGA treatment without a predictable pattern. These novel results describe the impact of WGA on low-biomass samples and may highlight issues to be aware of when designing future metagenomic studies that necessitate preceding WGA treatment.
