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

Ramiro Logares, Thomas H. A. Haverkamp, Surendra Kumar, Anders Lanzén, Alexander J. Nederbragt, Christopher Quince, Håvard Kauserud

Research output: Contribution to journalReview articlepeer-review

104 Citations (Scopus)


The 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.

Original languageEnglish
Pages (from-to)106-113
Number of pages8
JournalJournal of Microbiological Methods
Issue number1
Early online date28 Jul 2012
Publication statusPublished - Oct 2012


  • High-throughput sequencing
  • Illumina, 454, metagenomics
  • Metabolic-profiling
  • Microbial community
  • Taxonomic-profiling

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