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Normalization of environmental metagenomic DNA enhances the discovery of under‐represented microbial community members
Author(s) -
Ramond J.B.,
Makhalanyane T.P.,
Tuffin M.I.,
Cowan D.A.
Publication year - 2015
Publication title -
letters in applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.698
H-Index - 110
eISSN - 1472-765X
pISSN - 0266-8254
DOI - 10.1111/lam.12380
Subject(s) - metagenomics , biology , normalization (sociology) , computational biology , environmental dna , library , terminal restriction fragment length polymorphism , dna sequencing , genetics , dna , polymerase chain reaction , restriction fragment length polymorphism , gene , ecology , 16s ribosomal rna , biodiversity , sociology , anthropology
Abstract Normalization is a procedure classically employed to detect rare sequences in cellular expression profiles (i.e. c DNA libraries). Here, we present a normalization protocol involving the direct treatment of extracted environmental metagenomic DNA with S1 nuclease, referred to as normalization of metagenomic DNA : Nm DNA . We demonstrate that Nm DNA , prior to post hoc PCR ‐based experiments (16S rRNA gene T‐ RFLP fingerprinting and clone library), increased the diversity of sequences retrieved from environmental microbial communities by detection of rarer sequences. This approach could be used to enhance the resolution of detection of ecologically relevant rare members in environmental microbial assemblages and therefore is promising in enabling a better understanding of ecosystem functioning. Significance and Impact of the Study This study is the first testing ‘normalization’ on environmental metagenomic DNA (m DNA ). The aim of this procedure was to improve the identification of rare phylotypes in environmental communities. Using hypoliths as model systems, we present evidence that this post‐mDNA extraction molecular procedure substantially enhances the detection of less common phylotypes and could even lead to the discovery of novel microbial genotypes within a given environment.