MICROBIAL METAGENOMICS

Introduction: metagenomics as a new approach for the study of the microbial communities.
PART 1: Background.
Diversity of 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 Microbial Populations.
PART2 : The Species Concept.
Population Genomics Informs Our Understanding of the Bacterial Species Concept.
Metagenomic Approaches for the Identification of Microbial Species.
PART 3 : Metagenomics.
Microbial Ecology in the Age of Metagenomics.
Empirical Testing of 16S PCR Primer Pairs.
The Impact of Next‐Generation Sequencing Technologies on Metagenomics.
Accuracy and Quality of Massively Parallel DNA sequencing.
Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes.
Metagenomic Libraries for Functional Screening.
Towards Automated Phylogenomic Inference.
High‐Resolution Metagenomics: Assessing Specific Functional Types in Complex Microbial Communities.
Gene‐Targeted 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.
PART 4 : Consortia and Databases.
Soil Metagenomic Exploration of the Rare Biosphere.
The BIOSPAS Consortium: Soil Biology and Agricultural Production.
The Human Microbiome Project.
The Marine Microbiome Projects.
The Anaerobic Digestione Microbiome.
The Ribosomal Database Project: Sequences and Software for High‐Throughput rRNA Analysis.
The Metagenomics RAST Server.
The EBI Metagenomics Archive.
PART 5 : Computer‐Assisted Analysis.
Comparative Metagenome Analysis Using MEGAN.
Phylogenetic Binning of Metagenome Sequence Samples.
Iterative Read Mapping and Assembly Allows the Use of a More Distant Reference in Metagenome Assembly.
Ribosomal RNA Identification in Metagenomic and Metatranscriptomic Datasets.
SILVA: Comprehensive Databases for Quality Checked and Aligned Ribosomal RNA Sequence Data.
ARB: A Software Environment for Sequence Data.
The Phyloware Project: A Software Framework for Phylogenomic analysis.
MetaGene: Prediction of Prokaryotic and Phage Genes in Metagenomic Sequences.
Primers4clades: A Web Server to Design Lineage‐Specific PCR Primers for Gene‐Targeted Metagenomics.
ESPRIT: Estimating Species Richness Using Large Collections of 16S rRNA Data.
PART 6 : Complementary Approaches.
Metagenomic Approaches in Systems Biology.
Towards “Focused” Metagenomics: A Case Study Combining DNA Stable‐Isotope Probing, Multiple Displacement Amplification, and Metagenomics.
Suppressive Subtractive Hybridization Reveals Extensive Horizontal Transfer in the Rumen Metagenome.
PART 6A : Metatranscriptomics
Isolation of mRNA from Environmental Microbial Communities for Metatranscriptomic Analyses.
PART 6B : Metaproteomics.
Proteomics for the Analysis of Environmental Stress Responses in Prokaryotes.
Microbial Community Proteomics.
Synchronicity Between Population Structure and Proteome Profiles.
PART 6D : 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.
PART 6E : Single‐Cell Analysis.
Application of Cytomics to Separate Natural Microbial Communities.
Capturing Microbial Populations for Environmental Genomics.