title: New perspectives on microbial community distortion after whole-genome amplification.
abstract: 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 Betaproteobacteria showed a decrease in their abundance after WGA treatment. On the other hand, Enterobacteriaceae, an important biomarker group for fecal contamination in groundwater and drinking water, 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.
authors.affiliation: Department for Bioinformatics, Second Genome Inc., South San Francisco, California, United States of America.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Probst
authors.affiliation: Department for Bioinformatics, Second Genome Inc., South San Francisco, California, United States of America.
authors.forename: Thomas
authors.initials: T
authors.lastname: Weinmaier
authors.affiliation: Department for Bioinformatics, Second Genome Inc., South San Francisco, California, United States of America.
authors.forename: Todd Z
authors.initials: TZ
authors.lastname: DeSantis
authors.affiliation: U.S. Environmental Protection Agency, Cincinnati, Ohio, United States of America.
authors.forename: Jorge W
authors.initials: JW
authors.lastname: Santo Domingo
authors.affiliation: U.S. Environmental Protection Agency, Cincinnati, Ohio, United States of America.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Ashbolt
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D001482:Base Composition / Q000235:genetics; D018441:Biofilms; D017753:Ecosystem; D059646:Genome Size; D016680:Genome, Bacterial; D064307:Microbiota / Q000235:genetics*; D009584:Nitrogen / Q000378:metabolism; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D012722:Sewage / Q000382:microbiology
chemical_list: D012722:Sewage; D009584:Nitrogen