Culture-independent methods for studying environmental microorganisms: methods, application, and perspective

Diversity and phylogeny of bacteria on Zimbabwe tobacco leaves estimated by 16S rRNA sequence analysis

(2011) Can Su et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

High Abundance and Role of Antifungal Bacteria in Compost-Treated Soils in a Wildfire Area

(2011) Yong-Hak Kim et al.   MICROBIAL ECOLOGY

Diversity of Cervicovaginal Microbiota Associated with Female Lower Genital Tract Infections

(2011) Zongxin Ling et al.   MICROBIAL ECOLOGY

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

Phylogenetic analysis of the fecal flora of the wild pygmy loris

(2010) Xu Bo et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial diversities on unaged and aging flue-cured tobacco leaves estimated by 16S rRNA sequence analysis

(2010) Jingwen Huang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Diversity in the Archean Biosphere: New Insights from NanoSIMS

(2010) Dorothy Z. Oehler et al.   ASTROBIOLOGY

METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics

(2010) Johannes Goll et al.   BIOINFORMATICS

Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis

(2010) Emmanuelle Roth et al.   BMC MICROBIOLOGY

Distribution and Diversity of Bacteria in a Saline Meromictic Lake as Determined by PCR-DGGE of 16S rRNA Gene Fragments

(2010) Concetta Gugliandolo et al.   CURRENT MICROBIOLOGY

The Development and Stability of the Genus Bacteriodes from Human Gut Microbiota in HFA Mice Model

(2010) Jing Yuan et al.   CURRENT MICROBIOLOGY

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

(2010) Shaomei He et al.   ENVIRONMENTAL MICROBIOLOGY

Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems

(2010) Minou Nowrousian   EUKARYOTIC CELL

Bacterial diversity in the oral cavity of 10 healthy individuals

(2010) Elisabeth M Bik et al.   ISME Journal

Bacterial Community Diversity in the Brazilian Atlantic Forest Soils

(2010) Thiago Bruce et al.   MICROBIAL ECOLOGY

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

Human oral, gut, and plaque microbiota in patients with atherosclerosis

(2010) O. Koren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dormancy contributes to the maintenance of microbial diversity

(2010) S. E. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing

(2009) U. S. Sagaram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial composition and succession during storage of North-Atlantic cod (Gadus morhua) at superchilled temperatures

(2009) Eyjólfur Reynisson et al.   BMC MICROBIOLOGY

Bacterial diversity analysis of larvae and adult midgut micro-flora using culture-dependent and culture-independent methods in lab-reared and field-collected Anopheles stephensi-an Asian malarial vector

(2009) Asha Rani et al.   BMC MICROBIOLOGY

Bacterial communities in PAH contaminated soils at an electronic-waste processing center in China

(2009) Wen Zhang et al.   ECOTOXICOLOGY

Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity

(2009) Kenneth Wasmund et al.   FEMS MICROBIOLOGY ECOLOGY

Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA)

(2009) Annette Summers Engel et al.   ISME Journal

Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland

(2009) Karelyn Cruz-Martínez et al.   ISME Journal

16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis

(2009) Yunwei Wang et al.   ISME Journal

Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave

(2009) Yin Chen et al.   ISME Journal

Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine, South Dakota, USA

(2009) Gurdeep Rastogi et al.   JOURNAL OF MICROBIOLOGY

Microbial Diversity in Uranium Mining-Impacted Soils as Revealed by High-Density 16S Microarray and Clone Library

(2009) Gurdeep Rastogi et al.   MICROBIAL ECOLOGY

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

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

Monitoring Bacterial Community of Human Gut Microbiota Reveals an Increase in Lactobacillus in Obese Patients and Methanogens in Anorexic Patients

(2009) Fabrice Armougom et al.   PLoS One

High diversity of fungi in air particulate matter

(2009) J. Frohlich-Nowoisky 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

Broad-range PCR, cloning and sequencing of the full 16S rRNA gene for detection of bacterial DNA in synovial fluid samples of Tunisian patients with reactive and undifferentiated arthritis

(2009) Mariam Siala et al.   ARTHRITIS RESEARCH & THERAPY

T-RFLP-basedmcrAgene analysis of methanogenic archaea in association with oral infections and evidence of a novelMethanobrevibacterphylotype

(2009) M. E. Vianna et al.   Oral microbiology and immunology

Resolving Genetic Functions within Microbial Populations: In Situ Analyses Using rRNA and mRNA Stable Isotope Probing Coupled with Single-Cell Raman-Fluorescence In Situ Hybridization

(2008) W. E. Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS

(2008) S. Behrens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PCR-DGGE assessment of the bacterial diversity of breast milk in women with lactational infectious mastitis

(2008) Susana Delgado et al.   BMC INFECTIOUS DISEASES

Genomic sequencing of single microbial cells from environmental samples

(2008) Thomas Ishoey et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2008) Sarah M Sowell et al.   ISME Journal

Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces

(2008) Pauline D Scanlan et al.   ISME Journal

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Diversity of bacterial community in freshwater of Woopo wetland

(2008) Keun Sik Baik et al.   JOURNAL OF MICROBIOLOGY

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

The Airborne Metagenome in an Indoor Urban Environment

(2008) Susannah G. Tringe et al.   PLoS One

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

(2008) Anders F. Andersson et al.   PLoS One

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

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY

Intra-oral microbial profiles of beagle dogs assessed by checkerboard DNA–DNA hybridization using human probes

(2007) M. Rober et al.   VETERINARY MICROBIOLOGY