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Handbook of Molecular Microbial Ecology I

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

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.



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).


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...


Titel: Handbook of Molecular Microbial Ecology I
Untertitel: Metagenomics and Complementary Approaches
EAN: 9781118010440
ISBN: 978-1-118-01044-0
Digitaler Kopierschutz: Adobe-DRM
Format: E-Book (pdf)
Herausgeber: Wiley-Blackwell
Genre: Biologie
Anzahl Seiten: 800
Veröffentlichung: 18.05.2011
Jahr: 2011
Untertitel: Englisch
Dateigrösse: 13.9 MB