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Title

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

AuthorsLogares, Ramiro ; Haverkamp, Thomas H.A.; Kumar, Surendra; Lanzén, Anders; Nederbragt, Alexander J.; Quince, Christopher; Kauserud, Håvard
KeywordsIllumina
Taxonomic-profiling
Metabolic-profiling
Microbial community
High-throughput sequencing
454 pyrosequencing
Issue DateOct-2012
PublisherElsevier
CitationJournal of Microbiological Methods 91(1): 106-113 (2012)
AbstractThe incursion of High-Throughput Sequencing (HTS) in environmental microbiology brings unique opportunities and challenges. HTS now allows a high-resolution exploration of the vast taxonomic and metabolic diversity present in the microbial world, which can provide an exceptional insight on global ecosystem functioning, ecological processes and evolution. This exploration has also economic potential, as we will have access to the evolutionary innovation present in microbial metabolisms, which could be used for biotechnological development. HTS is also challenging the research community, and the current bottleneck is present in the data analysis side. At the moment, researchers are in a sequence data deluge, with sequencing throughput advancing faster than the computer power needed for data analysis. However, new tools and approaches are being developed constantly and the whole process could be depicted as a fast co-evolution between sequencing technology, informatics and microbiologists. In this work, we examine the most popular and recently commercialized HTS platforms as well as bioinformatics methods for data handling and analysis used in microbial metagenomics. This non-exhaustive review is intended to serve as a broad state-of-the-art guide to researchers expanding into this rapidly evolving field. © 2012 Elsevier B.V.
Description8 pages, 1 table
Publisher version (URL)http://dx.doi.org/10.1016/j.mimet.2012.07.017
URIhttp://hdl.handle.net/10261/90537
DOI10.1016/j.mimet.2012.07.017
Identifiersdoi: 10.1016/j.mimet.2012.07.017
issn: 0167-7012
e-issn: 1872-8359
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