Chapter 2
Metagenome Analysis
Anke Meyerdierks and Frank Oliver Glöckner
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. Meyerdierks (B)
Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
e-mail: ameyerdi@mpi-bremen.de
33
J.M. Cock et al. (eds.), Introduction to Marine Genomics,
Advances in Marine Genomics 1, DOI 10.1007/978-90-481-8639-6_2,
C
Springer Science+Business Media B.V. 2010
Metagenome Analysis
Anke Meyerdierks and Frank Oliver Glöckner
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. Meyerdierks (B)
Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
e-mail: ameyerdi@mpi-bremen.de
33
J.M. Cock et al. (eds.), Introduction to Marine Genomics,
Advances in Marine Genomics 1, DOI 10.1007/978-90-481-8639-6_2,
C
Springer Science+Business Media B.V. 2010