Handbook of molecular microbial ecology: 1 Metagenomics and complementary approaches
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | German |
| Veröffentlicht: |
Hoboken, NJ
Wiley-Blackwell
2011
|
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXII, 761 S. Ill., graph. Darst. |
| ISBN: | 9780470644799 9781118010518 |
Internformat
MARC
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| 008 | 110209s2011 ad|| |||| 00||| ger d | ||
| 020 | |a 9780470644799 |c hbk. |9 978-0-470-64479-9 | ||
| 020 | |a 9781118010518 |c oBook |9 978-1-118-01051-8 | ||
| 035 | |a (OCoLC)745478483 | ||
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| 084 | |a WG 4050 |0 (DE-625)148560: |2 rvk | ||
| 245 | 1 | 0 | |a Handbook of molecular microbial ecology |n 1 |p Metagenomics and complementary approaches |c ed. by F. J. De Bruijn |
| 264 | 1 | |a Hoboken, NJ |b Wiley-Blackwell |c 2011 | |
| 300 | |a XXII, 761 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 700 | 1 | |a Bruijn, Frans J. de |4 edt | |
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| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, EPUB |z 978-1-118-01049-5 |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, PDF |z 978-1-118-01044-0 |
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-021129218 | ||
Datensatz im Suchindex
| _version_ | 1804143816097136640 |
|---|---|
| adam_text | Contents
Preface
xv
Contributors
xvii
1.
Introduction
Frans
J.
de Bruijn
Part
1
Background Chapters
2. DNA
Reassociation
Yields Broad-Scale Information on Metagenome Complexity
and Microbial Diversity
5
Vigdis
L
Torsvik
and
Lise
0vreås
3.
Diversity of 23S rRNA Genes Within Individual Prokaryotic Genomes
17
Anna Pel William E.
Oberdorf,
Carlos W.
Nossa,
Pooja Chokshi, Martin J.
Blaser,
Living Yang, David M.
Rosmarin,
and Zhiheng Pei
4.
Use of the rRNA Operon and Genomic Repetitive Sequences for the Identification
of Bacteria
29
Andrea Maria
Amaral Nascimento
5.
Use of Different PCR Primer-Based Strategies for Characterization of Natural
Microbial Communities
41
James I. Prosser, Shahid Mahmood, and Thomas E.
Freitag
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
49
Qiongfang Li, Xiaoping Zhang, Ling
Zou, Qiang
Chen, David P. Fewer,
and
Kristina Lindström
7.
Amplified rDNA Restriction Analysis (ARDRA) for Identification and Phylogenetic
Placement of
lóS-rDNA
Clones
59
Menachem Y. Sklarz, Roey Angel, Osnat Gillor, and
Ines
M.
Soares
vii
viii Contents
8.
Clustering-Based
Peak Alignment Algorithm for Objective and Quantitative Analysis
of
DNA
Fingerprinting Data
67
Satoshi Ishii,
Koji Kadota,
and Keishi Senoo
Part
2
The Species Concept
9.
Population Genomics Informs Our Understanding of the Bacterial Species Concept
77
Margaret A. Riley
10.
The Microbial Pangenome: Implications for Vaccine Development
83
Annalisa Nuccitelli, Claudio
Donati, Michèle A. Barocchi,
and Riño Rappuoli
11.
Metagenomic Insights into Bacterial Species
89
Konstantinos
T. Konstantinidis
12.
Reports of Ad Hoc Committees for the
Réévaluation
of the Species Definition
in Bacteriology
99
Erko
Stackebrandt
13.
Metagenomic Approaches for the Identification of Microbial Species
105
David M. Ward,
Melanie
С.
Melendrez, Eric D. Becrafi, Christian G. Klatt, Jason M. Wood,
and Frederick M. Cohan
Part
3
Metagenomics
14.
Microbial Ecology in the Age of Metagenomics
113
Jianping Xu
15.
The Enduring Legacy of Small
Subunit rRNA
in Microbiology
123
Susannah G. Tringe and Philip Hugenholtz
16.
Pitfalls of PCR-Based rRNA Gene Sequence Analysis: An Update on Some Parameters
129
Erko
Stackebrandt
17.
Empirical Testing of 16S PCR Primer Pairs Reveals Variance in Target Specificity
and Efficacy not Suggested by In Silico Analysis
135
Sergio E. Morales and William E.
Holben
18.
The Impact of Next-Generation Sequencing Technologies on Metagenomics
143
George M.
Weinstock
19.
Accuracy and Quality of Massively Parallel
DNA Pyrosequencing
149
Susan M.
Huse
and David B. Mark Welch
Contents ix
20.
Environmental Shotgun Sequencing: Its Potential and Challenges for Studying
the Hidden World of Microbes
157
Jonathan A.
Eisen
21.
A Comparison of Random Sequence Reads Versus 16S rDNA Sequences
for Estimating the Biodiversity of a Metagenomic Sample
163
Chaysavanh Manichanh, Charles E. Chappie, Lionel Frangeul,
Karine Gloux,
Roderic Guigo, and Joel
Dore
22.
Metagenomic Libraries for Functional Screening
171
Trine Aakvik, Rahmi
Laie, Mark
Liles,
and Svein Valla
23.
GC Fractionation Allows Comparative Total Microbial Community Analysis, Enhances
Diversity Assessment, and Facilitates Detection of Minority Populations of Bacteria
183
William E.
Holben
24.
Enriching Plant Microbiota for a Metagenomic Library Construction
197
Ying
Zeng,
Hao-Xin Wang, Zhao-Liang Geng, and Yue-Mao Shen
25.
Towards Automated Phylogenomic Inference
205
Martin Wu and Jonathan A.
Eisen
26.
Integren
First Gene Cassettes: A Target to Find Adaptive Genes in Metagenomes
217
Lionel Huang and Christine Cagnon
27.
High-Resolution Metagenomics: Assessing Specific Functional Types in Complex
Microbial Communities
225
Ludmila Chistoserdova
28.
Gene-Targeted Metagenomics (GT Metagenomics) to Explore the Extensive Diversity
of Genes of Interest in Microbial Communities
235
Shoko Iwai, Benli
Chai,
Ederson da
С
Jesus,
С
Ryan Penton, Tae Kwon Lee,
James R. Cole, and James M. Tiedje
29.
Phylogenetic Screening of Metagenomic Libraries Using Homing Endonuclease
Restriction and Marker Insertion
245
Torsten
Thomas,
Staffan Kjelleberg,
and
Pui Yi
Yung
30.
ArrayOme- and tRNAcc-Facilitated Mobilome Discovery: Comparative
Genomics Approaches for Identifying Rich Veins of Bacterial Novel
DNA
Sequences
251
Hong-Yu
Ou
and Kumar Rajakumar
31.
Sequence-Based Characterization of Microbiomes by Serial Analysis
of Ribosomal Sequence Tags (SARST)
265
Zhongtang Yu and Mark Morrison
Contents
Part
4
Consortia and Databases
32.
The Metagenomics of Plant Pathogen-Suppressive Soils
277
Jan Dirk van
Elsas,
Anna Maria Kieiak. and Mariana Silvia Cretoiu
33.
Soil Metagenomic Exploration of the Rare Biosphere
287
Tom O. Delmont,
Laure Franqiteville,
Samuel Jacquiod, Pascal
Simonét,
and Timothy M.
Vogel
34.
The BIOSPAS Consortium: Soil Biology and Agricultural Production
299
Luis Gabriel Wall
35.
The Human Microbiome Project
307
George M.
Weinstock
36.
The Ribosomal Database Project: Sequences and Software
for High-Throughput rRNA Analysis
313
James R. Cole, Qiong Wang, Benli
Chai,
and James M. Tiedje
37.
The Metagenomics
RAST
Server: A Public Resource for the Automatic
Phylogenetic and Functional Analysis of Metagenomes
325
Elizabeth M. Glass and Folker Meyer
38.
The
EBI
Metagenomics Archive, Integration and Analysis Resource
333
C. Hunter, G. Cochrane, R. Apweiler, S. Hunter
Part
5
Computer-Assisted Analysis
39.
Comparative Metagenome Analysis Using MEGAN
343
Daniel H. Huson and
Suparna
Mitra
40.
Phylogenetic Binning of Metagenome Sequence Samples
353
Alice Carolyn McHardy and Kaustubh Paul
41.
Gene Prediction in Metagenomic Fragments with Orphelia: A Large-Scale
Machine Learning Approach
359
Katharina
H.
Hoff, Maike Tech, Thomas Lingner, Rolf Daniel,
Burkhard Morgenstern, and Peter Meinicke
42.
Binning
Metagenomic
Sequences Using Seeded GSOM
369
Ching-Hung Tseng, Chon-Kit
Kenneth
Chan, Arthur L. Hsiu
Saman
К.
Halgamuge,
and Sen-Lin Tang
Contents xi
43. Iterative
Read Mapping and Assembly Allows the Use of a More Distant
Reference in Metagenome Assembly
379
Bas E.
Duti/li
Martija A. Hiiynen,
J
olein Gloerich, am! Marc
Straus
44. Ribosomal
RNA
Identification in Metagenomic and Metatranscriptomic Datasets 387
Ying Huang,
Weizhong
Li,
Patricia W.
Finn,
and David
L
Perkins
45. SILVA:
Comprehensive Databases for Quality Checked and Aligned Ribosomal
RNA
Sequence Data Compatible with
ARB 393
Elmar Prüsse,
Christian
Quast,
Pelin
Yilmaz, Wolfgang Ludwig, Jörg
Peplies,
and Frank Oliver
Glöckner
46. ARB:
A Software Environment for Sequence Data
399
Ralf Westram, Kai Bader, Elmar
Prüsse, Yadhii
Kumar,
Harald
Meier,
Frank
Oliver Glöckner,
and Wolfgang
Ludwig
47.
The Phyloware Project: A Software Framework for Phylogenomic Virtue
407
Daniel
N.
Frank and Charles E. Robertson
48.
MetaSim: A Sequencing Simulator for Genomics and Metagenomics
417
Daniel
С
Richter,
Felix
Ott,
Alexander
F. Auch,
Ramona
Schmid,
and Daniel
H. Husou
49.
ClustScan: An Integrated Program Package for the Detection and
Semiautomatic Annotation of Secondary Metabolite Clusters in Genomic
and Metagenomic
DNA Datasets
423
John
Cullimi.
Antonio Starcevic,
Janko
Dinünk;
Jurka Zucko.
Paul
F. Long,
and Daslav Hranueli
50. MetaGene:
Prediction of Prokaryotic and Phage Genes
in Metagenomic Sequences
433
Hideki Noguchi
51.
Primers4clades: A Web Server to Design Lineage-Specific PCR Primers
for Gene-Targeted Metagenomics
441
Bernardo Sachman-Ruiz, Bruno Contreras-Moreira, Enrique Zoz.aya,
Cristina
Martínez-Garza,
and Pablo Vinuesa
52.
A Parsimony Approach to Biological Pathway Reconstruction/Inference
for Metagenomes
453
Yuzhen Ye and Thomas G. Doak
53.
ESPRIT: Estimating Species Richness Using Large Collections
of 16S rRNA Data
461
Yijun Sun, Yunpeng
Cai,
Li Liu. Fahong Yu, and William
Farmene
хн
Contents
Part
6
Complementary Approaches
54.
Metagenomic Approaches in Systems Biology
475
Maria-Eugenia Guazzaroni and Manuel Ferrer
55.
Towards Focused Metagenomics: A Case Study Combining
DNA
Stable-Isotope
Probing, Multiple Displacement Amplification, and Metagenomics
491
Yin Chen, Marc G. Dumont, Joshua D.
Neufeld,
and J. Colin Murrell
56.
Suppressive Subtractive Hybridization Reveals Extensive Horizontal Transfer
in the Rumen Metagenome
497
Elizabeth A. Galbraith, Dionysios A. Antonopoulos, Karen E. Nelson, and Bryan A. White
Part 6A Microarrays
57.
GeoChip: A High-Throughput Metagenomics Technology for Dissecting
Microbial Community Functional Structure
509
Joy D. van Nostrand, Zhili He, and Jizhong Zhou
58.
Phylogenetic Microarrays (PhyloChips) For Analysis of Complex
Microbial Communities
521
Eoin L. Brodie
59.
Phenomics and Phenotype Microarrays: Applications
Complementing Metagenomics
533
Barry R. Bochner
60.
Microbial Persistence in Low-Biomass, Extreme Environments: The Great Unknown
541
Parag Vaishampayan, James
N.
Benardini, Myron T. La Due, and
Kasthuri Venkateswaran
61.
Application of Phylogenetic Oligonucleotide Microarrays in Microbial Analysis
551
Pankaj Trivedi and
Nian Wang
Part 6B Metatranscriptomics
62.
Isolation of mRNA From Environmental Microbial Communities
for Metatranscriptomic Analyses S69
Peer M.
Schenk
63.
Comparative Day/Night Metatranscriptomic Analysis of Microbial Communities
in the North Pacific Subtropical Gyre
____________________________________________575
Rachel S. Poretsky and Mary Ann
Moran
Contents xiii
64.
The Double-RNA Approach to Simultaneously Assess the Structure and Function
of a Soil Microbial Community
587
Tim Urich and
Christa Schleper
65.
Soil Eukaryotic Diversity: A Metatranscriptomic Approach
597
Roland Marmeisse, Julie Bailly, Coralie Damon, Frederic Lehembre, Marc Lemaire,
Micheline Wésolowski-Louvel,
and Laurence Fraissinet-Tachet
Part 6C Metaproteomics
66.
Proteomics for the Analysis of Environmental Stress Responses in Prokaryotes
605
Ksenia J. Groh, Victor J. Nesatyy, and Marc J.-F. Suter
67.
Microbial Community Proteomics
627
Paul Wilmes
68.
Synchronicity between Population Structure and Proteome
Proflies:
A Metaproteomic Analysis of Chesapeake Bay Bacterial Communities
637
Jinjun Kan, Thomas E. Hanson, and Feng Chen
69.
High-Throughput Cyanobacterial Proteomics: Systems-Level Proteome
Identification and Quantitation
645
Saw Yen Ow and Phillip
С
Wright
70.
Protein Expression Profile of an Environmentally Important Bacterial Strain:
The
Chromáte
Response of Arthrobacter Species Strain FB24
663
Kristene L.
Henne,
Joshua E. Turse, Cindy H. Nakatsu, and Allan
E. Konôpka
Part 6D Metabolomics
71.
The Small-Molecule Dimension: Mass-spectrometry-based Metabolomics,
Enzyme Assays, and Imaging
677
Trent R. Northen
72.
Metabolomics: High-Resolution Tools Offer to Follow Bacterial Growth
on a Molecular Level
___________________________________________________________683
Lucio
Marianna,
Agnes
Fekete,
Moritz Frommberger,
and Philippe Schmitt-Kopplin
73.
Metabolic Profiling of Plant Tissues by Electrospray Mass Spectrometry
697
Heather Walker
74.
Metabolite Identification, Pathways, and Omic Integration Using Online
Databases and Tools
__________________________________________________________ 709
Matthew P. Davey
xiv Contents
Part 6E Single-Cell Analysis
75.
Application of Cytomics to Separate Natural Microbial Communities
by their Physiological Properties
727
Susann Müller
and David R. Johnson
76.
Capturing Microbial Populations for Environmental Genomics
735
Martha Schattenhofer and Annelie
Wendeberg
77.
Microscopic Single-Cell Isolation and Multiple Displacement
Amplification of Genomes from Uncultured Prokaryotes
741
Peter
Westermann
and Thomas
Kvist
Index
747
|
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| id | DE-604.BV037215235 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:53:34Z |
| institution | BVB |
| isbn | 9780470644799 9781118010518 |
| language | German |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-021129218 |
| oclc_num | 745478483 |
| open_access_boolean | |
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| physical | XXII, 761 S. Ill., graph. Darst. |
| publishDate | 2011 |
| publishDateSearch | 2011 |
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| publisher | Wiley-Blackwell |
| record_format | marc |
| spelling | Handbook of molecular microbial ecology 1 Metagenomics and complementary approaches ed. by F. J. De Bruijn Hoboken, NJ Wiley-Blackwell 2011 XXII, 761 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Bruijn, Frans J. de edt (DE-604)BV037215185 1 Erscheint auch als Online-Ausgabe, EPUB 978-1-118-01049-5 Erscheint auch als Online-Ausgabe, PDF 978-1-118-01044-0 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021129218&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Handbook of molecular microbial ecology |
| title | Handbook of molecular microbial ecology |
| title_auth | Handbook of molecular microbial ecology |
| title_exact_search | Handbook of molecular microbial ecology |
| title_full | Handbook of molecular microbial ecology 1 Metagenomics and complementary approaches ed. by F. J. De Bruijn |
| title_fullStr | Handbook of molecular microbial ecology 1 Metagenomics and complementary approaches ed. by F. J. De Bruijn |
| title_full_unstemmed | Handbook of molecular microbial ecology 1 Metagenomics and complementary approaches ed. by F. J. De Bruijn |
| title_short | Handbook of molecular microbial ecology |
| title_sort | handbook of molecular microbial ecology metagenomics and complementary approaches |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021129218&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV037215185 |
| work_keys_str_mv | AT bruijnfransjde handbookofmolecularmicrobialecology1 |