For those interested in microbial diversity and/or metagenomics there are two volumes that are coming out soon that are of interest:
- Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches.
- Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats
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:
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” (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).
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).