Metagenomic Analyses: Past and Future Trends

Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria

(2010) J. W. Craig et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Product-Induced Gene Expression, a Product-Responsive Reporter Assay Used To Screen Metagenomic Libraries for Enzyme-Encoding Genes

(2010) T. Uchiyama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Community Dynamics of Bacteria in Sourdough Fermentations as Revealed by Their Metatranscriptome

(2010) S. Weckx et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Hitherto Unknown [Fe-Fe]-Hydrogenase Gene Diversity in Anaerobes and Anoxic Enrichments from a Moderately Acidic Fen

(2010) O. Schmidt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity of Glycosyl Hydrolases from Cellulose-Depleting Communities Enriched from Casts of Two Earthworm Species

(2010) A. Beloqui et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic Analysis of Apple Orchard Soil Reveals Antibiotic Resistance Genes Encoding Predicted Bifunctional Proteins

(2010) J. J. Donato et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments

(2010) Meng Li et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Use of metagenomic approaches to isolate lipolytic genes from activated sludge

(2010) Ren-Bao Liaw et al.   BIORESOURCE TECHNOLOGY

Recent progress and new challenges in metagenomics for biotechnology

(2010) Ludmila Chistoserdova   BIOTECHNOLOGY LETTERS

Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers

(2010) Bin Yang et al.   BMC BIOINFORMATICS

Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context

(2010) Rita Bartossek et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomic array analysis of ‘Candidatus Accumulibacter phosphatis’-enriched enhanced biological phosphorus removal sludge

(2010) Shaomei He et al.   ENVIRONMENTAL MICROBIOLOGY

A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry

(2010) J.D. Rudney et al.   Molecular Oral Microbiology

A metagenomic  -glucuronidase uncovers a core adaptive function of the human intestinal microbiome

(2010) K. Gloux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isolation and Characterization of Metalloproteases with a Novel Domain Structure by Construction and Screening of Metagenomic Libraries

(2009) T. Waschkowitz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Discovery of [NiFe] Hydrogenase Genes in Metagenomic DNA: Cloning and Heterologous Expression in Thiocapsa roseopersicina

(2009) G. Maroti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of a Novel Alkaliphilic Esterase Active at Low Temperatures by Screening a Metagenomic Library from Antarctic Desert Soil

(2009) C. Heath et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Rapid Identification of Genes Encoding DNA Polymerases by Function-Based Screening of Metagenomic Libraries Derived from Glacial Ice

(2009) C. Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Abundance of Novel and Diverse tfdA-Like Genes, Encoding Putative Phenoxyalkanoic Acid Herbicide-Degrading Dioxygenases, in Soil

(2009) A. Zaprasis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Deep Sequencing of a Dimethylsulfoniopropionate-Degrading Gene (dmdA) by Using PCR Primer Pairs Designed on the Basis of Marine Metagenomic Data

(2009) V. A. Varaljay et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome

(2009) E. J. Biers et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DNA-Stable Isotope Probing Integrated with Metagenomics for Retrieval of Biphenyl Dioxygenase Genes from Polychlorinated Biphenyl-Contaminated River Sediment

(2009) W. J. Sul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome

(2009) C. Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Isolation and Identification of Cellulose-Binding Proteins from Sheep Rumen Contents

(2009) A. Toyoda et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms

(2009) D. S. A. Goltsman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking

(2009) Sho Morimoto et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Achievements and new knowledge unraveled by metagenomic approaches

(2009) Carola Simon et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes

(2009) Aurélien Tartar et al.   Biotechnology for Biofuels

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Methods for comparative metagenomics

(2009) Daniel H Huson et al.   BMC BIOINFORMATICS

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre

(2009) Rachel S. Poretsky et al.   ENVIRONMENTAL MICROBIOLOGY

Novel blue light-sensitive proteins from a metagenomic approach

(2009) G. P. Pathak et al.   ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil

(2009) Karin Hjort et al.   FEMS MICROBIOLOGY ECOLOGY

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment

(2009) Shoko Iwai et al.   ISME Journal

Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens

(2009) C.-J. Duan et al.   JOURNAL OF APPLIED MICROBIOLOGY

Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing

(2009) Magdalena Kröber et al.   JOURNAL OF BIOTECHNOLOGY

Lipase Diversity in Glacier Soil Based on Analysis of Metagenomic DNA Fragments and Cell Culture

(2009) Yuhong Zhang   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column

(2009) Yanmei Shi et al.   NATURE

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Lysine racemase: a novel non-antibiotic selectable marker for plant transformation

(2009) I-Chieh Chen et al.   PLANT MOLECULAR BIOLOGY

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

(2009) N. Delmotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environmental proteomics: Analysis of structure and function of microbial communities

(2009) Thomas Schneider et al.   PROTEOMICS

A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles

(2009) Angel Angelov et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters

(2008) Jack A. Gilbert et al.   ENVIRONMENTAL MICROBIOLOGY

Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation

(2008) Vincent J. Denef et al.   ENVIRONMENTAL MICROBIOLOGY

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea

(2008) Sarah M Sowell et al.   ISME Journal

Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal

(2008) Paul Wilmes et al.   ISME Journal

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Identification of Novel Esterase from Metagenomic Library of Yangtze River

(2008) Baolin Sun   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Advances in Recovery of Novel Biocatalysts from Metagenomes

(2008) Helen L. Steele et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Metagenomics for Mining New Genetic Resources of Microbial Communities

(2008) Manuel Ferrer et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Metagenomics

(2008) R.D. Sleator et al.   LETTERS IN APPLIED MICROBIOLOGY

Characterization and its Potential Application of Two Esterases Derived from the Arctic Sediment Metagenome

(2008) Jeong Ho Jeon et al.   MARINE BIOTECHNOLOGY

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

(2008) Chaysavanh Manichanh et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment

(2008) Paul Wilmes et al.   PLoS One

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

(2008) Jack A. Gilbert et al.   PLoS One

Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment

(2008) J. F. Biddle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application of metaproteomic analysis for studying extracellular polymeric substances (EPS) in activated sludge flocs and their fate in sludge digestion

(2008) C. Park et al.   WATER SCIENCE AND TECHNOLOGY