Handbook of Molecular Microbial Ecology I Metagenomics and Complementary Approaches

by de Bruijn, Frans J.

• ISBN13: 9780470644799
• ISBN10: 0470644796
• Edition: 1st
• Format: Hardcover
• Copyright: 2011-07-26
• Publisher: Wiley-Blackwell

Summary

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.

Author Biography

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.

Table of Contents

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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