Handbook of Molecular Microbial Ecology I Metagenomics and Complementary Approaches
, by de Bruijn, Frans J.Note: Supplemental materials are not guaranteed with Rental or Used book purchases.
- ISBN: 9780470644799 | 0470644796
- Cover: Hardcover
- Copyright: 7/26/2011
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.
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.
Preface | |
Contributors | |
Introduction | |
Background Chapters | |
DNA reassociation yields broad-scale information on metagenome complexity and microbial diversity | |
Diversity of 23S rRNA genes within individual prokaryotic genomes | |
Use of the rRNA operon and genomic repetitive sequences for the identification of bacteria | |
Use of different PCR primer-based strategies for characterization of natural microbial communities | |
Horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plants Astragalus luteolus and Astragalus ernestii in Sichuan, China | |
Amplified rDNA restriction analysis (ARDRA)for identification and phylogenetic placement of 16S-rDNA clones | |
Clustering-based peak alignment algorithm for objective and quantitative analysis of DNA fingerprinting data | |
The Species Concept | |
Population genomics informs our understanding of the bacterial species concept | |
Genome analysis of Streptococcus agalactiae: Implication for the microbial "pan-genome" | |
Metagenomic insights into bacterial species | |
Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology | |
Metagenomic Approaches for the Identification of Microbial Species | |
Metagenomics | |
Microbial Ecology in the age of metagenomics | |
The enduring legacy of small rRNA in microbiology | |
Pitfalls of PCR-based rRNA gene sequence analysis: an update on some parameters | |
Empirical testing of 16S rRNA gene PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis | |
The impact of next-generation sequencing technologies on (meta)genomics | |
Accuracy and quality of massively parallel DNA pyrosequencing | |
Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes | |
Comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library | |
Metagenomic libraries for functional screeing | |
GC Fractionation Allows Comparative Total Microbial Community Analysis, Enhances Diversity Assessment, and Facilitates of Minority Populations of Bacteria | |
Enriching plant microbiota for a metagenomic library construction | |
Towards Automated Phylogenomic Inference | |
Integron first gene cassettes: a target to find adaptive genes in metagenomes | |
High-resolution metagenomics: assessing specific functional types in complex microbial communities | |
Gene-targeted -metagenomics (GT-metagenomics) to explore the extensive diversity of genes of interest in microbial communities | |
Phylogenetic screening of metagenomic libraries using homing endonuclease restriction and marker insertion | |
ArrayOme- & tRNAcc-facilitated mobilome discovery: comparative genomics approaches for identifying rich veins of novel bacterial DNA sequences | |
Sequence-Based Characterization of Microbiomes by Serial Analysis of Ribosomal Sequence Tags (SARST) | |
Consortia and Databases | |
The metagenomics of plant pathogen-suppressive soils | |
Soil Metagenomic Exploration of the Rare Biosphere | |
The BIOSPAS consortium: Soil Biology and agricultural production | |
The Human Microbiome Project | |
The Ribosomal Database Project: sequences and Software for high-throughput rRNA analysis | |
The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes | |
The EBI Metagenomics Archive, Integration and Analysis resource | |
Computer Assisted Analysis | |
Comparative metagenome analysis using MEGAN | |
Phylogenetic binning of metagenome sequence samples | |
Gene prediction in metagenomic fragments with Orphelia: A large scale machine learning approach | |
Binning metagenomic sequences using seeded GSOm | |
Iterative read mapping and assembly allows the use of a more distant reference in metagenomic assembly | |
Ribosomal RNA identification in metagenomic and metatranscriptomic datasets | |
SILVA: comprehensive databases for quality checked and aligned ribosomal RNA sequence data compatible with ARB | |
ARB; a software environment for sequence data | |
The Phyloware Project: A software framework for phylogenomic virtue | |
Metasim- A sequencing simulator for genomics and metagenomics | |
ClustScan: an integrated program package for the detection and semi-automatic annotation of secondary metabolite clusters in genomic and metagenomic DNA datasets | |
MetaGene; Prediction of prokaryotic and phage genes in metagenomic sequences | |
primers4clades, a web server to design lineage-specific PCR primers for gene-targeted metagenomics | |
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes | |
ESPRIT: estimating species richness using large collections of 16S rRNA data | |
Complementary Approaches | |
(Meta) genomics approaches in systems biology | |
Towards "focused metagenomics": a case study combining DNA stable-isotope probing, multiple displacement amplification and metagenomics | |
Galbraith, E. A., D. A. Antonopoulos, K. E. Nelson, and B. A. White . Suppressive subtractive hybridization reveals extensive horizontal transfer in the rumen metagenome | |
Microarrays | |
GeoChip: A high throughout metagenomics technology for dissecting microbial community functional structure | |
Phylogenetic microarrays (PhyloChips) for analysis of complex microbial communities | |
Phenomics and Phenotype MicroArrays: Applications Complementing Metagenomics | |
Microbial persistence in low biomass, extreme environments: The great unknown | |
Application of phylogenetic oligonucleotide microarrays in microbial analysis | |
Metatranscriptomics | |
Isolation of mRNA from environmental microbial communities for metatranscriptomic analyses | |
Comparative day/night metatrancriptomic analysis of microbial communities in the North Pacific subtropical gyre | |
The "double RNA" approach to simultaneously assess the structure and function of environmental microbial communities by meta-transcriptomics | |
Soil eukaryotic diversity, a metatranscriptomic approach | |
Metaproteomics | |
Proteomics for the analysis of environmental stress responses in prokaryotes | |
Microbial community proteomics | |
Synchronicity between population structure and proteome profiles: A metaproteomic analysis of Chesapeake Bay bacterial communities | |
High-Throughput Cyanobacterial Proteomics: Systems-level Proteome Identification and Quantitation | |
Protein Expression Profile of an Environmentally Important Bacterial Strain: the Chromate Response of Arthrobacter sp. strain FB24 | |
Metabolomics | |
The small molecule dimension: Mass spectrometry based metabolomics, enzyme assays, and imaging | |
Metabolomics: high resolution tools offer to follow bacterial growth on a molecular level | |
Metabolic profiling of plant tissues by electrospray mass spectrometry | |
Metabolite identification, pathways and omic integration using online databases and tools | |
Single cell analysis | |
Application of cytomics to separate natural microbial communities by their physiological properties | |
Capturing microbial populations for environmental genomics | |
Microscopic single-cell isolation and multiple displacement amplification of genomes from uncultured prokaryotes | |
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