A survey of the methods for the characterization of microbial consortia and communities (Q36222841)

12 August 2017

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title

A survey of the methods for the characterization of microbial consortia and communities (English)

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12 August 2017

3

Charles W Greer

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12 August 2017

1

Dan Spiegelman

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12 August 2017

Gavin Whissell

2

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12 August 2017

1 May 2005

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Canadian Journal of Microbiology

12 August 2017

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12 August 2017

51

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12 August 2017

5

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12 August 2017

355-386

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Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis

12 August 2017

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Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants

21 January 2018

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Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment

21 January 2018

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Changes in the Lactobacillus community during Ricotta forte cheese natural fermentation.

21 January 2018

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Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content.

21 January 2018

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Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream

21 January 2018

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Portable system for microbial sample preparation and oligonucleotide microarray analysis

21 January 2018

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Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes

21 January 2018

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Strong, weak, and missing links in a microbial community of the N.W. Mediterranean Sea

21 January 2018

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Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park

21 January 2018

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Anaerobic biodegradation of squalene: Using DGGE to monitor the isolation of denitrifying Bacteria taken from enrichment cultures

21 January 2018

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Characterization of the bacterial community of a zinc-polluted soil.

21 January 2018

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Streptococcus suis serotypes characterized by analysis of chaperonin 60 gene sequences

21 January 2018

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Metabolomics: quantification of intracellular metabolite dynamics

21 January 2018

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Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics.

21 January 2018

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Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries

21 January 2018

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Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays

21 January 2018

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Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input.

21 January 2018

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Quantitative detection of microbial genes by using DNA microarrays

21 January 2018

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Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source

21 January 2018

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Isoprenoid Quinones in the Classification of Coryneform and Related Bacteria

21 January 2018

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Environmental application of array technology: promise, problems and practicalities

21 January 2018

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Characterization of the bacterial consortium associated with black band disease in coral using molecular microbiological techniques.

21 January 2018

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Molecular evaluation of microbial diversity occurring in different types of Mozzarella cheese.

21 January 2018

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rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity.

21 January 2018

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Natural attenuation of chlorinated solvents at Area 6, Dover Air Force Base: characterization of microbial community structure

21 January 2018

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Factors affecting the robustness of metabolite fingerprinting using 1H NMR spectra.

21 January 2018

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Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms

21 January 2018

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Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis

21 January 2018

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Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose

21 January 2018

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Metabolomics – the link between genotypes and phenotypes

21 January 2018

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Molecular microbial ecology: land of the one-eyed king

21 January 2018

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How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity

21 January 2018

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Characterization of microbial communities using randomly amplified polymorphic DNA (RAPD).

21 January 2018

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Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns

21 January 2018

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Relative effectiveness of kinetic analysis vs single point readings for classifying environmental samples based on community-level physiological profiles (CLPP).

21 January 2018

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Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells

21 January 2018

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Detection of the dipicolinic acid biomarker in Bacillus spores using Curie-point pyrolysis mass spectrometry and Fourier transform infrared spectroscopy.

21 January 2018

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Psychrophilic and psychrotrophic microorganisms.

21 January 2018

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Deconvolution gas chromatography/mass spectrometry of urinary organic acids--potential for pattern recognition and automated identification of metabolic disorders

21 January 2018

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Extensive profiling of a complex microbial community by high-throughput sequencing

21 January 2018

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cpnDB: a chaperonin sequence database

21 January 2018

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Quinone profiles in lake sediments: Implications for microbial diversity and community structures.

21 January 2018

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Phylogeny and photosynthetic features of Thiobacillus acidophilus and related acidophilic bacteria: its transfer to the genus Acidiphilium as Acidiphilium acidophilum comb. nov.

21 January 2018

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A new structural type of methionaquinones isolated from hot spring sulfur-turf bacterial mats

21 January 2018

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Toward the bioremediation of dioxin-polluted soil: structural and functional analyses of in situ microbial populations by quinone profiling and culture-dependent methods

21 January 2018

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DNA‐based monitoring of total bacterial community structure in environmental samples

21 January 2018

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Plant functional genomics

21 January 2018

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Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples

21 January 2018

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Diversity and structure of the archaeal community in the leachate of a full-scale recirculating landfill as examined by direct 16S rRNA gene sequence retrieval

21 January 2018

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Identifying microbial diversity in the natural environment: a molecular phylogenetic approach.

21 January 2018

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Microbial diversity along a transect of agronomic zones.

21 January 2018

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Taxonomic Study of Lactobacillus mali Carr and Davis 1970 and Related Strains: Validation of Lactobacillus mali Carr and Davis 1970 over Lactobacillus yamanashiensis Nonomura 1983

21 January 2018

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Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis

21 January 2018

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Sulfate-reducing bacterial community response to carbon source amendments in contaminated aquifer microcosms

21 January 2018

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Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer

21 January 2018

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Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology.

21 January 2018

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The Use of Carbon Substrate Utilization Patterns in Environmental and Ecological Microbiology

21 January 2018

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DNA-microarrays and food-biotechnology

21 January 2018

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Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses

21 January 2018

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Molecular characterization of microbial community in nitrate-removing activated sludge

21 January 2018

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Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment

21 January 2018

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Characterization of microbial community in granular sludge treating brewery wastewater

21 January 2018

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Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment

21 January 2018

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Distribution and Composition of Microbial Populations in a Landfill Leachate Contaminated Aquifer (Grindsted, Denmark).

21 January 2018

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Sensitive characterization of microbial ubiquinones from biofilms by electrospray/mass spectrometry

21 January 2018

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Characterization of metal-resistant soil eubacteria by polymerase chain reaction--denaturing gradient gel electrophoresis with isolation of resistant strains.

21 January 2018

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A new version of the RDP (Ribosomal Database Project).

21 January 2018

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Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms

21 January 2018

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Characterization of contaminating DNA in Taq polymerase which occurs during amplification with a primer set for Legionella 5S ribosomal RNA.

21 January 2018

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Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products.

21 January 2018

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Composition and physiological profiling of sprout-associated microbial communities.

21 January 2018

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Factors affecting reproducibility of random amplified polymorphic DNA fingerprinting.

21 January 2018

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DNA recombination during PCR.

21 January 2018

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Detection of catabolic genes in indigenous microbial consortia isolated from a diesel-contaminated soil.

21 January 2018

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Taxonomic and functional diversity of pseudomonads isolated from the roots of field-grown canola.

21 January 2018

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Molecular characterization of the Lactobacillus community in traditional processing of Mozzarella cheese

21 January 2018

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Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes

21 January 2018

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Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology.

21 January 2018

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Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis

21 January 2018

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Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis

21 January 2018

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Microbial ecology and evolution: a ribosomal RNA approach

21 January 2018

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N2-Fixing Microbial Consortia Associated with the Ice Cover of Lake Bonney, Antarctica

21 January 2018

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Viability of soil bacteria: Optimization of plate-counting technique and comparison between total counts and plate counts within different size groups

21 January 2018

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Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms

21 January 2018

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Detection of methanotrophs with highly divergent pmoA genes from Arctic soils

21 January 2018

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Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes

21 January 2018

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Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria

21 January 2018

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Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes.

21 January 2018

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Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints

21 January 2018

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Field-scale C-labeling of phospholipid fatty acids (PLFA) and dissolved inorganic carbon: tracing acetate assimilation and mineralization in a petroleum hydrocarbon-contaminated aquifer.

21 January 2018

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A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations

21 January 2018

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Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking

21 January 2018

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Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment

21 January 2018

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Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability

21 January 2018

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Characterization of microbial communities in anaerobic bioreactors using molecular probes

21 January 2018

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Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin

21 January 2018

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21 January 2018

NMR-based metabolomics

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Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization

21 January 2018

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Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques

21 January 2018

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Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil

21 January 2018

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Characterizing aquatic bacteria according to population, cell size, and apparent DNA content by flow cytometry

21 January 2018

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Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms

21 January 2018

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Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts

21 January 2018

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Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys

21 January 2018

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Bacterial diversity in maize rhizospheres: conclusions on the use of genetic profiles based on PCR-amplified partial small subunit rRNA genes in ecological studies

21 January 2018

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Metagenomic profiling: microarray analysis of an environmental genomic library

21 January 2018

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An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization

21 January 2018

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Association of microbial community composition and activity with lead, chromium, and hydrocarbon contamination

21 January 2018

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Hybrid DNA artifact from PCR of closely related target sequences.

21 January 2018

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Microbial diversity and activity along the forefields of two receding glaciers

21 January 2018

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Bacterial succession in glacial forefield soils characterized by community structure, activity and opportunistic growth dynamics

21 January 2018

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Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays

21 January 2018

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Microbial ubiquinones: multiple roles in respiration, gene regulation and oxidative stress management

21 January 2018

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Characterization of bacterial consortia capable of degrading 4-chlorobenzoate and 4-bromobenzoate under denitrifying conditions

21 January 2018

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Generation of entire human papillomavirus genomes by long PCR: frequency of errors produced during amplification

21 January 2018

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Characterization of microbial communities from coastal waters using microarrays.

21 January 2018

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Plant metabolomics: large-scale phytochemistry in the functional genomics era.

21 January 2018

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The deconvolution of pyrolysis mass spectra using genetic programming: application to the identification of some Eubacterium species.

21 January 2018

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Application of metabolomics to plant genotype discrimination using statistics and machine learning

21 January 2018

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Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and Archaea in the deep ocean.

21 January 2018

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Molecular techniques for determining microbial diversity and community structure in natural environments

21 January 2018

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Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system

21 January 2018

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Molecular characterization of a salt-tolerant bacterial community in the rice rhizosphere

21 January 2018

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Community structure and metabolism through reconstruction of microbial genomes from the environment

21 January 2018

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Characterization of depth-related population variation in microbial communities of a coastal marine sediment using 16S rDNA-based approaches and quinone profiling

21 January 2018

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Nutrigenomics: exploiting systems biology in the nutrition and health arena

21 January 2018

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Nucleic acid amplification strategies for DNA microarray-based pathogen detection

21 January 2018

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Toward the implementation of metabolomic assessments of human health and nutrition

21 January 2018

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Comparative analysis of polychlorinated biphenyl-dechlorinating communities in enrichment cultures using three different molecular screening techniques

21 January 2018

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Analysis of the microbial functional diversity within water-stressed soil communities by flow cytometric analysis and CTC+ cell sorting

21 January 2018

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DNA polymorphisms amplified by arbitrary primers are useful as genetic markers

21 January 2018

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Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulon

21 January 2018

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Molecular typing techniques to characterize the development of a lactic acid bacteria community on vacuum-packaged beef.

21 January 2018

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Identification of single bacterial cells using digoxigenin-labelled, rRNA-targeted oligonucleotides

21 January 2018

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Phospholipid fatty acid profiles in selected members of soil microbial communities

21 January 2018

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Spatial and resource factors influencing high microbial diversity in soil

21 January 2018

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Microbial diversity and heterogeneity in sandy subsurface soils

21 January 2018

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A molecular approach to search for diversity among bacteria in the environment

21 January 2018

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Combined microbial community-level analyses for quality assurance of terrestrial subsurface cores

21 January 2018

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A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints

21 January 2018

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Plant metabolomics: the missing link in functional genomics strategies

21 January 2018

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Variation of Microbial Rhizosphere Communities in Response to Crop Species, Soil Origin, and Inoculation with Sinorhizobium meliloti L33

21 January 2018

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The Sensitivity of Single-Strand Conformation Polymorphism Analysis for the Detection of Single Base Substitutions

21 January 2018

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An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry

21 January 2018

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Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria

21 January 2018

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Characterization of the microbial community of lotic organic aggregates ('river snow') in the Elbe River of Germany by cultivation and molecular methods

21 January 2018

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An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics

21 January 2018

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Analysis of Broad-scale Differences in Microbial Community Composition of Two Pristine Forest Soils

21 January 2018

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16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils

21 January 2018

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21 January 2018

Identifiers

DOI

10.1139/W05-003

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12 August 2017

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PubMed ID

16088332