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.

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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)