Frans J. de Bruijn

Handbook of Molecular Microbial Ecology I

Metagenomics and Complementary Approaches

• Gebundenes Buch

Produktbeschreibung

Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches is the first comprehensive reference covering the various metagenomics in a large variety of habitats, which could not previously have been analysed without metagenomic methodology. This Volume includes topics such as species designations in microbiology, metagenomics, consortia and databases, bioinformatics, microarrays, and other metagenomics applications. This reference is ideal for researchers in metagenomics, microbiology, environmental microbiology, those working on the Human Microbiome Project, microbial geneticists, molecular microbiology, and bioinformatics.

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The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats

Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds.

Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This first volume, Metagenomics and Complementary Approaches, covers such topics as:
Background information on DNA reassociation and use of 16 rRNA and other DNA fingerprinting approaches
Species designation in microbiology
Metagenomics: Introduction to the basic tools with examples
Consortia and databases
Bioinformatics
Computer-assisted analysis
Complementary approaches-microarrays, metatranscriptomics, metaproteomics, metabolomics, and single cell analysis

A special feature of this volume is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies.

Handbook of Molecular Microbial Ecology I is an invaluable reference for researchers in metagenomics, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; molecular microbial ecologists; and professionals in molecular microbiology and bioinformatics.

Produktdetails

• Verlag: Wiley & Sons
• Artikelnr. des Verlages: 14564479000
• 1. Auflage
• Seitenzahl: 800
• Erscheinungstermin: 26. Juli 2011
• Englisch
• Abmessung: 286mm x 226mm x 41mm
• Gewicht: 2340g
• ISBN-13: 9780470644799
• ISBN-10: 0470644796
• Artikelnr.: 32568332

Autorenporträt

Frans J. de Bruijn received his Ph.D. (Cellular and Developmental Biology; Microbial Genetics) from Harvard University in 1983. His resume reflects an array of experiences as a teacher, researcher, board member and a plethora of other accomplishments. He is currently Director of Research at the Laboratory for Plant-Microbe Interactions in Toulouse, France.

Inhaltsangabe

Preface. Contributors. 1. Introduction (Frans J. de Bruijn). Background
Chapters. 2. DNA reassociation yields broad-scale information on metagenome
complexity and microbial diversity (V. Torsvik). 3. Diversity of 23S rRNA
genes within individual prokaryotic genomes (Zhiheng Pei). 4. Use of the
rRNA operon and genomic repetitive sequences for the identification of
bacteria (A. Nascimento). 5. Use of different PCR primer-based strategies
for characterization of natural microbial communities (James Prosser). 6.
Horizontal gene transfer and recombination shape mesorhizobial populations
in the gene center of the host plants Astragalus luteolus and Astragalus
ernestii in Sichuan, China (Xiaoping Zhang). 7. Amplified rDNA restriction
analysis (ARDRA)for identification and phylogenetic placement of 16S-rDNA
clones (Menachim Sklarz). 8. Clustering-based peak alignment algorithm for
objective and quantitative analysis of DNA fingerprinting data (Satoshi
Ishii). The Species Concept. 9. Population genomics informs our
understanding of the bacterial species concept (Margaret Riley). 10. Genome
analysis of Streptococcus agalactiae: Implication for the microbial
"pan-genome" (R. Rappuoli). 11. Metagenomic insights into bacterial species
(Kostas Konstantinidis). 12. Report of the ad hoc committee for the
re-evaluation of the species definition in bacteriology (E. Stackebrandt).
13. Metagenomic Approaches for the Identification of Microbial Species
(David Ward). Metagenomics. 14. Microbial Ecology in the age of
metagenomics (Jianping Xu). 15. The enduring legacy of small rRNA in
microbiology (Susan Tringe). 16. Pitfalls of PCR-based rRNA gene sequence
analysis: an update on some parameters (Stackebrandt). 17. Empirical
testing of 16S rRNA gene PCR primer pairs reveals variance in target
specificity and efficacy not suggested by in silico analysis (Sergio
Morales and Bill Holben). 18. The impact of next-generation sequencing
technologies on (meta)genomics (George Weinstock). 19. Accuracy and quality
of massively parallel DNA pyrosequencing (Susan Huse and David Mark Welch).
20. Environmental shotgun sequencing: Its potential and challenges for
studying the hidden world of microbes (Jonathan Eisen). 21. Comparison of
random sequence reads versus 16S rDNA sequences for estimating the
biodiversity of a metagenomic library (C. Manischan). 22. Metagenomic
libraries for functional screeing (Svein Valla). 23. GC Fractionation
Allows Comparative Total Microbial Community Analysis, Enhances Diversity
Assessment, and Facilitates of Minority Populations of Bacteria (Bill
Holben). 24. Enriching plant microbiota for a metagenomic library
construction (Ying Zeng). 25. Towards Automated Phylogenomic Inference (Wu
and Eisen). 26. Integron first gene cassettes: a target to find adaptive
genes in metagenomes (Christine Cagnon). 27. High-resolution metagenomics:
assessing specific functional types in complex microbial communities
(Christoserdova). 28. Gene-targeted -metagenomics (GT-metagenomics) to
explore the extensive diversity of genes of interest in microbial
communities (J. Tiedje). 29. Phylogenetic screening of metagenomic
libraries using homing endonuclease restriction and marker insertion
(Torsten Thomas). 30. ArrayOme- & tRNAcc-facilitated mobilome discovery:
comparative genomics approaches for identifying rich veins of novel
bacterial DNA sequences (Hong-Yu OU). 31. Sequence-Based Characterization
of Microbiomes by Serial Analysis of Ribosomal Sequence Tags (SARST)
(Zhongtang Yu). Consortia and Databases. 32. The metagenomics of plant
pathogen-suppressive soils (J.D. Van Elsas). 33. Soil Metagenomic
Exploration of the Rare Biosphere (Pascal Simonet and Timothy Vogel). 34.
The BIOSPAS consortium: Soil Biology and agricultural production (Luis
Wall). 35. The Human Microbiome Project (George Weinstock). 36. The
Ribosomal Database Project: sequences and Software for high-throughput rRNA
analysis (J. R. Cole, G. M. Garrity and Jim Tiedje). 37. The metagenomics
RAST server- a public resource for the automatic phylogenetic and
functional analysis of metagenomes (Folker Meyer). 38. The EBI Metagenomics
Archive, Integration and Analysis resource (Apweiler). Computer Assisted
Analysis. 39. Comparative metagenome analysis using MEGAN (Suparna Mitra
and Daniel Huson). 40. Phylogenetic binning of metagenome sequence samples
(Alice C. McHardy). 41. Gene prediction in metagenomic fragments with
Orphelia: A large scale machine learning approach (Katharina Hoff). 42.
Binning metagenomic sequences using seeded GSOm (Sen-Lin Tang). 43.
Iterative read mapping and assembly allows the use of a more distant
reference in metagenomic assembly (Bas E. Dutilh). 44. Ribosomal RNA
identification in metagenomic and metatranscriptomic datasets (Li). 45.
SILVA: comprehensive databases for quality checked and aligned ribosomal
RNA sequence data compatible with ARB (Frank Gloeckner). 46. ARB; a
software environment for sequence data (Wolfgang Ludwig). 47. The Phyloware
Project: A software framework for phylogenomic virtue (Daniel Frank). 48.
Metasim- A sequencing simulator for genomics and metagenomics (Daniel
Richter). 49. ClustScan: an integrated program package for the detection
and semi-automatic annotation of secondary metabolite clusters in genomic
and metagenomic DNA datasets (Daslav Hranueli). 50. MetaGene; Prediction of
prokaryotic and phage genes in metagenomic sequences (Noguchi). 51.
primers4clades, a web server to design lineage-specific PCR primers for
gene-targeted metagenomics (Pablo Vinuesa). 52. A parsimony approach to
biological pathway reconstruction/inference for genomes and metagenomes (Y.
Ye). 53. ESPRIT: estimating species richness using large collections of 16S
rRNA data (Yijun Sun). Complementary Approaches. 54. (Meta) genomics
approaches in systems biology (Manuel Ferrer). 55. Towards "focused
metagenomics": a case study combining DNA stable-isotope probing, multiple
displacement amplification and metagenomics (J. Colin Murrell). 56.
Galbraith, E. A., D. A. Antonopoulos, K. E. Nelson, and B. A. White .
Suppressive subtractive hybridization reveals extensive horizontal transfer
in the rumen metagenome (Bryan White). Microarrays. 57. GeoChip: A high
throughout metagenomics technology for dissecting microbial community
functional structure (J. Zhou). 58. Phylogenetic microarrays (PhyloChips)
for analysis of complex microbial communities (Eoin Brodie). 59. Phenomics
and Phenotype MicroArrays: Applications Complementing Metagenomics (Barry
Bochner). 60. Microbial persistence in low biomass, extreme environments:
The great unknown (Kasthuri Venkateswaran). 61. Application of phylogenetic
oligonucleotide microarrays in microbial analysis (Nian Wang).
Metatranscriptomics. 62. Isolation of mRNA from environmental microbial
communities for metatranscriptomic analyses (P. Schenk). 63. Comparative
day/night metatrancriptomic analysis of microbial communities in the North
Pacific subtropical gyre (Rachel Poretski). 64. The "double RNA" approach
to simultaneously assess the structure and function of environmental
microbial communities by meta-transcriptomics (Tim Urich and Christa
Schleper). 65. Soil eukaryotic diversity, a metatranscriptomic approach
(Marmeisse). Metaproteomics. 66. Proteomics for the analysis of
environmental stress responses in prokaryotes (Mark Suter). 67. Microbial
community proteomics (Paul Wilmes). 68. Synchronicity between population
structure and proteome profiles: A metaproteomic analysis of Chesapeake Bay
bacterial communities (Feng Chen). 69. High-Throughput Cyanobacterial
Proteomics: Systems-level Proteome Identification and Quantitation (Phillip
Wright). 70. Protein Expression Profile of an Environmentally Important
Bacterial Strain: the Chromate Response of Arthrobacter sp. strain FB24 (K.
Henne). Metabolomics. 71. The small molecule dimension: Mass spectrometry
based metabolomics, enzyme assays, and imaging (Trent R. Northen). 72.
Metabolomics: high resolution tools offer to follow bacterial growth on a
molecular level (Lucio Marianna and Philipp Schmitt-Kopplin). 73. Metabolic
profiling of plant tissues by electrospray mass spectrometry (Heather
Walker). 74. Metabolite identification, pathways and omic integration using
online databases and tools (Matthew Davey). Single cell analysis. 75.
Application of cytomics to separate natural microbial communities by their
physiological properties (Susann Müller). 76. Capturing microbial
populations for environmental genomics (A. Pernthaler/Wendeberg). 77.
Microscopic single-cell isolation and multiple displacement amplification
of genomes from uncultured prokaryotes (Peter Westermann).

Rezensionen

"Handbook of Molecular Microbial Ecology I is an invaluable reference for researchers in metagenomics, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; molecular microbial ecologists; and professionals in molecular microbiology and bioinformatics." (Bois et Forets des Tropiques, 2011)

"Handbook of Molecular Microbial Ecology I is an invaluable reference for researchers in metagenomics, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; molecular microbial ecologists; and professionals in molecular microbiology and bioinformatics." (TMCnet.com, 8 November 2011)