Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and...

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Vydané v:Applied microbiology and biotechnology Ročník 80; číslo 3; s. 365 - 380
Hlavní autori: Schütte, Ursel M. E, Abdo, Zaid, Bent, Stephen J, Shyu, Conrad, Williams, Christopher J, Pierson, Jacob D, Forney, Larry J
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Berlin/Heidelberg Berlin/Heidelberg : Springer-Verlag 01.09.2008
Springer Berlin Heidelberg
Springer
Springer Nature B.V
Predmet:
16S rRNA genes
Archaea
Archaea - genetics
Automation
Bacteria
Bacteria - classification
Bacteria - genetics
Biological and medical sciences
Biotechnology
Change detection
classification
Cloning
Composition
DNA Fingerprinting
DNA Fingerprinting - methods
DNA Primers
DNA Primers - genetics
DNA, Ribosomal
DNA, Ribosomal - genetics
Environmental Microbiology
Enzymes
Fingerprinting
Fundamental and applied biological sciences. Psychology
Fungi
Fungi - genetics
Genes
genetics
Internet
labor
Life Sciences
methods
Microbial activity
Microbial communities
Microbial Genetics and Genomics
Microbiological Techniques
Microbiological Techniques - methods
Microbiology
Microbiomes
Microorganisms
Mini-Review
Multivariate statistics
Noise
Polymerase chain reaction
Polymorphism
Polymorphism, Restriction Fragment Length
researchers
Restriction fragment length polymorphism
Ribonucleic acid
ribosomal RNA
RNA
RNA, Ribosomal, 16S
RNA, Ribosomal, 16S - genetics
rRNA 16S
Statistical analysis
Statistical methods
Statistics
Studies
T-RFLP
temporal variation
Temporal variations
Microbial communities
Multivariate statistics
T-RFLP
16S rRNA genes
T-RFLP .Microbial communities
Restriction fragment length polymorphism
Gene
Ribosomal RNA
16S-RNA
Statistics
Microbial community
ISSN:0175-7598, 1432-0614, 1432-0614
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Abstract Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.
AbstractList Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies. [PUBLICATION ABSTRACT]
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.
Author Abdo, Zaid
Bent, Stephen J
Shyu, Conrad
Pierson, Jacob D
Schütte, Ursel M. E
Forney, Larry J
Williams, Christopher J
Author_xml – sequence: 1
  fullname: Schütte, Ursel M. E
– sequence: 2
  fullname: Abdo, Zaid
– sequence: 3
  fullname: Bent, Stephen J
– sequence: 4
  fullname: Shyu, Conrad
– sequence: 5
  fullname: Williams, Christopher J
– sequence: 6
  fullname: Pierson, Jacob D
– sequence: 7
  fullname: Forney, Larry J
BackLink http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20605593$$DView record in Pascal Francis
https://www.ncbi.nlm.nih.gov/pubmed/18648804$$D View this record in MEDLINE/PubMed
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Keywords Microbial communities
Multivariate statistics
T-RFLP
16S rRNA genes
T-RFLP .Microbial communities
Restriction fragment length polymorphism
Gene
Ribosomal RNA
16S-RNA
Statistics
Microbial community
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  doi: 10.1111/j.1365-294X.2005.02842.x
– volume: 54
  start-page: 121
  year: 2003
  ident: 1565_CR44
  publication-title: J Microbiol Methods
  doi: 10.1016/S0167-7012(03)00003-4
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Snippet Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the...
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SubjectTerms 16S rRNA genes
Archaea
Archaea - genetics
Automation
Bacteria
Bacteria - classification
Bacteria - genetics
Biological and medical sciences
Biotechnology
Change detection
classification
Cloning
Composition
DNA Fingerprinting
DNA Fingerprinting - methods
DNA Primers
DNA Primers - genetics
DNA, Ribosomal
DNA, Ribosomal - genetics
Environmental Microbiology
Enzymes
Fingerprinting
Fundamental and applied biological sciences. Psychology
Fungi
Fungi - genetics
Genes
genetics
Internet
labor
Life Sciences
methods
Microbial activity
Microbial communities
Microbial Genetics and Genomics
Microbiological Techniques
Microbiological Techniques - methods
Microbiology
Microbiomes
Microorganisms
Mini-Review
Multivariate statistics
Noise
Polymerase chain reaction
Polymorphism
Polymorphism, Restriction Fragment Length
researchers
Restriction fragment length polymorphism
Ribonucleic acid
ribosomal RNA
RNA
RNA, Ribosomal, 16S
RNA, Ribosomal, 16S - genetics
rRNA 16S
Statistical analysis
Statistical methods
Statistics
Studies
T-RFLP
temporal variation
Temporal variations
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Title Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities
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