Binga EK, Lasken RS, Neufeld JD.. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J 2: 233-241

Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
The ISME Journal (Impact Factor: 9.3). 04/2008; 2(3):233-41. DOI: 10.1038/ismej.2008.10
Source: PubMed


Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

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    • "Care must be taken in interpreting diversity estimates calcu - lated from the data . First , evenness can be influenced by the use of MDA , which can unevenly amplify the initial template ( Dean et al . , 2001 ) , be biased toward small circular ssDNA molecules and form chimeras ( Binga et al . , 2008 ; Polson et al . , 2011 ) ."
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    • "Gene-targeted sequencing based on PCR amplification technique is able to analyse the minute amounts of template DNA recovered in forensic samples. The need for a relatively large amount of initial DNA template for shotgun sequencing makes this approach less suitable for forensic oriented metagenomic analysis but whole-genome amplification (WGA), using Phi 29 DNA polymerase, represents an effective way of enabling whole-genome shotgun sequencing from small quantities of DNA [29]. "
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    • "This breakthrough was enabled by the development of the MDA reaction (Dean et al., 2001, 2002), which can amplify a single genome copy more than a billion fold enabling sequencing of DNA from very low (femtogram) levels (about the amount of DNA in a single bacterial cell). Bacteria that have not been cultivated by conventional culturing techniques are currently the central target of single-cell genomics (Lasken et al., 2005; Raghunathan et al., 2005; Hutchison and Venter, 2006; Ishoey et al., 2008; Lasken, 2012) The recent advancements in DNA sequencing of single bacterial cells has accelerated the study of uncultivated microbes (Lasken, 2012), providing genomic assemblies for species previously known only from 16S rRNA clone libraries and metagenomic data (Marcy et al., 2007; Podar et al., 2007; Binga et al., 2008; Eloe et al., 2011; Youssef et al., 2011; Dupont et al., 2012; McLean et al., 2013a; Nurk et al., 2013b; Rinke et al., 2013). Using these approaches, the so-called “dark matter of life” which represents uncultivated microbes and even entire divisions of bacterial phyla (candidate divisions and candidate phyla) are slowly being revealed with assembled genomes. "
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