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Genotypic Microbial Community Profiling: A Critical Technical Review

Microbial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning an... Full description

Journal Title: Microbial ecology 2007-08-01, Vol.54 (2), p.276-289
Main Author: NOCKER, Andreas
Other Authors: BURR, Mark , CAMPER, Anne K
Format: Electronic Article Electronic Article
Language: English
Subjects:
DNA
Publisher: New York, NY: Springer Science + Business Media, Inc
ID: ISSN: 0095-3628
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title: Genotypic Microbial Community Profiling: A Critical Technical Review
format: Article
creator:
  • NOCKER, Andreas
  • BURR, Mark
  • CAMPER, Anne K
subjects:
  • Animal, plant and microbial ecology
  • Archaea - genetics
  • Bacteria - genetics
  • Biodiversity
  • Biological and medical sciences
  • Chromatography, High Pressure Liquid
  • Cloning, Molecular
  • Communities
  • DNA
  • DNA, Ribosomal - genetics
  • Electrophoresis
  • Electrophoresis, Polyacrylamide Gel
  • Fundamental and applied biological sciences. Psychology
  • Fungi - genetics
  • Gels
  • General aspects
  • Genetic Techniques
  • Genotype
  • Microbial ecology
  • Microbiological Techniques - methods
  • Phylogenetics
  • Polymerase Chain Reaction
  • Polymorphism, Restriction Fragment Length
  • Polymorphism, Single-Stranded Conformational
  • Product category rules
  • Restriction fragment length polymorphism
  • Ribosomal DNA
  • Sequencing
ispartof: Microbial ecology, 2007-08-01, Vol.54 (2), p.276-289
description: Microbial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.
language: eng
source:
identifier: ISSN: 0095-3628
fulltext: no_fulltext
issn:
  • 0095-3628
  • 1432-184X
url: Link


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descriptionMicrobial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.
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subjectAnimal, plant and microbial ecology ; Archaea - genetics ; Bacteria - genetics ; Biodiversity ; Biological and medical sciences ; Chromatography, High Pressure Liquid ; Cloning, Molecular ; Communities ; DNA ; DNA, Ribosomal - genetics ; Electrophoresis ; Electrophoresis, Polyacrylamide Gel ; Fundamental and applied biological sciences. Psychology ; Fungi - genetics ; Gels ; General aspects ; Genetic Techniques ; Genotype ; Microbial ecology ; Microbiological Techniques - methods ; Phylogenetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single-Stranded Conformational ; Product category rules ; Restriction fragment length polymorphism ; Ribosomal DNA ; Sequencing
ispartofMicrobial ecology, 2007-08-01, Vol.54 (2), p.276-289
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abstractMicrobial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.
copNew York, NY
pubSpringer Science + Business Media, Inc
pmid17345133
doi10.1007/s00248-006-9199-5