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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Vydáno v:	Applied microbiology and biotechnology Ročník 80; číslo 3; s. 365 - 380
Hlavní autoři:	Schütte, Ursel M. E, Abdo, Zaid, Bent, Stephen J, Shyu, Conrad, Williams, Christopher J, Pierson, Jacob D, Forney, Larry J
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Berlin/Heidelberg Berlin/Heidelberg : Springer-Verlag 01.09.2008 Springer Berlin Heidelberg Springer Springer Nature B.V
Témata:	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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Popis
Shrnutí:	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.
Bibliografie:	http://dx.doi.org/10.1007/s00253-008-1565-4 ObjectType-Article-1 SourceType-Scholarly Journals-1 content type line 14 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 ObjectType-Undefined-1 ObjectType-Feature-3 ObjectType-Review-4
ISSN:	0175-7598 1432-0614 1432-0614
DOI:	10.1007/s00253-008-1565-4