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Abstract

The term “metagenomics” represents a combination of molecular and bioinformatic tools used to assess the genetic information of a community without prior cultivation of the individual species. It is valuable for the study of microorganisms of which only a minor fraction is yet culturable. The collective genomes present in an environmental sample or in an enrichment of target cells are extracted and subject to sequence-based or functional analyses. The field of metagenomics is evolving very rapidly, especially due to newly developed high-throughput sequencing technologies and increased computational power. Metatranscriptome and – proteome analyses are increasingly combined with metagenomic studies in order to assess not only the genetic potential of a microbial community, but also the genes expressed in a particular environment. The present chapter gives a short historical overview of the early years of metagenome analyses, and of possible applications. Challenges regarding the molecular and bioinformatic part of metagenome analyses are discussed. The molecular section includes strategies to access a metagenome. Methods to enrich for cells or the DNA of certain subpopulations prior to metagenome analysis, as well as to extract, purify and amplify DNA are given. The construction and sequence-based screening of small and large insert metagenomic libraries as well as a library-independent metagenomic approach using a new high throughput sequencing technology are described. The bioinformatic section provides an overview of assembly and binning tools, gene prediction programs, and annotation systems. This section also addresses the problem of metagenomic studies on habitats with high microbial diversity. Moreover, approaches to analyse phylogenetic and functional diversity within a dataset are discussed. The aim of the chapter is to provide the reader with basic information on both the molecular and bioinformatic aspects of metagenome analysis, to give hints to further reading and, therefore, to enable the reader to use this valuable method in an appropriate way in his or her studies. A.