Friday, June 03, 2011

Crosspost from http://microBE.net: New, massive volumes on #metagenomics coming out soon

For those interested in microbial diversity and/or metagenomics there are two volumes that are coming out soon that are of interest:
Edited by Frans J. de Bruijn these two volumes are the most comprehensive coverage of metagenomics out there right now. The chapters are almost overwhelming (full disclosure, I have two chapters in here - both of which are republications of Open Access papers I have published on metagenomics).  See below for full chapter lists.

Order from Amazon:
Volume I: Metagenomics and Complementary Approached
  • 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” (Rino 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 (Erko 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 (Erko 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 Ksenia Groh, Victor Nesatyy and Marc 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).
Volume 2: Metagenomics in Different Habitats
  • 1. Introduction (Frans J. de Bruijn).
  • Viral Genomes.
    • 2. Viral metagenomics (Shannon Williamson).
    • 3. Methods in Viral Metagenomics (Thurber).
    • 4. Metagenomic contrasts of viruses in soil and aquatic environments (Eric Wommack).
    • 5. Biodiversity and biogeography of phages in modern stromatolites and thromolites (Christelle Desnues).
    • 6. Assembly of Viral Metagenomes from Yellowstone Hot Springs Reveals Phylogenetic Relationships and Host Co-Evolution (Thomas Schoenfeld).
    • 7. Next-generation sequencing and metagenomic analysis; a universal diagnostic tool in plant pathology (Ian Adams).
    • 8. Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High-throughput Sequencing Approach (T. Nakaya).
  • The Soil Habitat.
    • 9. Soil based Metagenomics (R. Daniel).
    • 10. Methods in Metagenomic DNA, RNA and Protein Isolation from Soil (P. Gunasharan).
    • 11. Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications (Mark Liles).
    • 12. Application of PCR-DGGE and metagenome walking to retrieve full-length functional genes from soil (Morimoto).
    • 13. Actinobacterial diversity associated with Antarctic Dry Valley mineral soils (Cowan).
    • 14. Targetting major soil-borne bacterial lineages using large-insert metaenomic approaches (G. Kowalchuk).
    • 15. Novelty and uniqueness patterns of rare members of the soil biosphere (M. Elshahed).
    • 16. Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters (Holben WE).
    • 17. The Antibiotic Resistance: Origins, Diversity, and Future Prospects (Gerard Wright).
  • The Digestive Tract.
    • 18. Functional Intestinal Metagenomics (Michael Kleerebezem).
    • 19. Assessment and improvement of methods for microbial DNA preparation from fecal Samples (M. Hattori).
    • 20. Role of dysbiosis in inflammatory bowel diseases (Johan Dicksved).
    • 21. Culture independent analysis of the human gut microbiota and its activities (Kieran Tuohi).
    • 22. Complete genome of an uncultured endowsymbiont coupling nitrogen fixation to cellulolysis with protest cells in termite gut (Hongo).
    • 23. Cloning and identification of genes encoding acidic cellulases from metagenomes of buffalo rumen (Feng).
  • Marine and Lakes.
    • 24. Microbial diversity in the deep seas and the underexplored “rare biosphere” (David Mark Welsch and Susan Huse).
    • 25. Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord (Steven J. Hallam).
    • 26. Adaptation to nutrient availability in marine microorganisms by gene gain and loss (A. Martini).
    • 27. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities (Jack Gilbert).
    • 28. Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a lacustrine ecosystem (Didier Debroas).
    • 29. Metagenomics of the marine subsurface: the first glimpse from the Peru Margin, ODP Site 122 (Jennifer Biddle).
    • 30. A targeted metagenomic approach to determine the ‘population genome’ of marine Synechoccus (D. J. Scanlan).
    • 31. Diversity and role of bacterial integron/gene cassette metagenome in extreme marine environments (Hosam Easa Elsaied and Akihiko Maruyama).
  • Other Habitats.
    • 32. The Olavius algarvensis metagenome revisited: lessons learned from the analysis of the low diversity microbial consortium of a gutless marine worm (Nicole Dubulier).
    • 33. Microbiome diversity in human saliva (Ivan Nasidze).
    • 34. Approaches to understanding population level functional diversity in a microbial community (D. Bhaya).
    • 35. A functional metagenomic approach for discovering nickel resistance genes from the rhizosphere of an acid mine drainage environment (JOSE Gonzales –Pastor).
    • 36. The Microbiome of Leaf-cutter Ant Fungus Gardens (Garret Suen).
    • 37. Diversity of archaea in terrestrial hot springs and role In ammonia oxidation (Chuanlun Zhang).
    • 38. Colinization of nascent, deep-sea hydrothermal vents by a novel Archaeal and Nanoarchaeal assemblage (S. Craig Cary).
    • 39. Analysis of the Metagenome from a biogas-producing microbial Community by means of Bioinformatucs Methods (Andreas Schlueter).
    • 40. Amplicon pyrosequencing analysis of endosymbiont population structure (Colleen Kavahagh).
    • 41. Investigative bacterial diversity along alkaline hot spring thermal gradients by barcoded pyrosequencing (Scott Miller and Michael Welzer).
    • 42. Genetic characterization of microbial communities living at the surface of building stones (J. C. Salvado).
    • 43. Novel aromatic degradation pathway genes and their organization as revealed by metagenomic analysis (Kentaro).
    • 44. Functional screening of a wide host-range metagenomic library from a wastewater treatment plant yields a novel alcohol/aldehyde dehydrogenase (Wexler).
    • 45. Aromatic hydrocarbon degradation genes from chronically polluted Subantarctic marine sediments (H. M. Dionisi).
    • 46. Isolation and characterization if alkane hydroxylases from a metagenomic llibrary of Pacific deep-sea sediment  (Fengping Wang).
  • Biocatalysts and Natural Products.
    • 47. Emerging Fields in Functional Metagenomics and its Industrial Relevance  - Overcoming Limitations and Redirecting the Search for Novel Biocatalysts (Wolfgang Streit).
    • 48. Carboxylesterases and Lipases from Metagenomes (Chow and Wolfgang Streit).
    • 49. Expanding small molecule functional megenomics through parallel screening of broad host-range cosmid environmental DNA libraries in diverse Proteobacteria (Sean Brady).
    • 50. Biomedicinals from the microbial metagenomes of marine invertebrates (Walter Dunlap).
    • 51. Molecular characterization of TEM-type beta-Lactamases identified in Cold-seep sediments of Edison Seamount (South of Lihir Island).
    • 52. Identification of Novel Bioactive Compounds from the Metagenome of the Marine (David Lejon).
    • 53. Functional Viral Metagenomics and the Development of New Enzymes for DNA and RNA Amplification and Sequencing (Thomas Schoenfeld).
  • Summary.
    • 54. Future of metagenomics, metatranscriptomics, metabolomics, metaproteomics and single cell analysis: A perspective (J. Tiedje).
    • 55. Darwin in the 21st Century: Natural Selection, Molecular Biology, and Species Concepts (Francisco Ayala).

1 comment:

  1. Dear Jonathan, thanks very much for the nice Blog about the Metagenomics Books!! I know that they are a bit overwhelming, but once I got started I just could not stop! Best Wishes! Frans

    ReplyDelete