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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| Veröffentlicht in: | Applied microbiology and biotechnology 2008-09, Vol.80 (3), p.365-380 |
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| creator | Schütte, Ursel M. E Abdo, Zaid Bent, Stephen J Shyu, Conrad Williams, Christopher J Pierson, Jacob D Forney, Larry J |
| description | 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. |
| doi_str_mv | 10.1007/s00253-008-1565-4 |
| format | Article |
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Psychology</subject><subject>Fungi - genetics</subject><subject>Genes</subject><subject>Life Sciences</subject><subject>Microbial activity</subject><subject>Microbial communities</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbiological Techniques - methods</subject><subject>Microbiology</subject><subject>Mini-Review</subject><subject>Multivariate statistics</subject><subject>Noise</subject><subject>Polymerase chain reaction</subject><subject>Polymorphism</subject><subject>Polymorphism, Restriction Fragment Length</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Statistical analysis</subject><subject>Statistical methods</subject><subject>Studies</subject><subject>T-RFLP</subject><issn>0175-7598</issn><issn>1432-0614</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kc2KFDEUhQtRnHb0AdxoEBRdlN78dmrZDDMqNCrT4zqkU6nqDJWkJ6kS2sfwiSdNNQ64cBVCvnPuPTlV9RLDRwyw_JQBCKc1gKwxF7xmj6oFZpTUIDB7XC0AL3m95I08q57lfAuAiRTiaXWGpWBSAltUf1btLx2MzcgFNO4smrJFsUOjTd4FPaBk85icGV0MqEu69zaMaLChH3doH4eDj2m_c9mj9zf19dX6xweki-yQXT7aYLFB6frbCvU2lBljRGankzbF3v22yDuT4taVMSZ6PwU3OpufV086PWT74nSeV5ury5uLL_X6--evF6t1bZhsxho3jIJp2600HJdLR7AgHeV4S8iy0ZwIujRcAmVWCyKlaGQHshWM8lZjel69m133Kd5NJaTyLhs7DDrYOGUlGsZxMS7gm3_A2zilkjErQhoBDAQpEJ6hkifnZDu1T87rdFAY1LErNXelSlfq2JViRfPqZDxtvW0fFKdyCvD2BOhs9FB-PxiX_3IEBHDe0MKRmcvlKfQ2PWz4v-mvZ1Gno9J9KsY_NwQwBWiIZJjTe_mLtIE</recordid><startdate>20080901</startdate><enddate>20080901</enddate><creator>Schütte, Ursel M. 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E</au><au>Abdo, Zaid</au><au>Bent, Stephen J</au><au>Shyu, Conrad</au><au>Williams, Christopher J</au><au>Pierson, Jacob D</au><au>Forney, Larry J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities</atitle><jtitle>Applied microbiology and biotechnology</jtitle><stitle>Appl Microbiol Biotechnol</stitle><addtitle>Appl Microbiol Biotechnol</addtitle><date>2008-09-01</date><risdate>2008</risdate><volume>80</volume><issue>3</issue><spage>365</spage><epage>380</epage><pages>365-380</pages><issn>0175-7598</issn><eissn>1432-0614</eissn><coden>AMBIDG</coden><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.</abstract><cop>Berlin/Heidelberg</cop><pub>Berlin/Heidelberg : Springer-Verlag</pub><pmid>18648804</pmid><doi>10.1007/s00253-008-1565-4</doi><tpages>16</tpages></addata></record> |
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| subjects | 16S rRNA genes Archaea - genetics Automation Bacteria - classification Bacteria - genetics Biological and medical sciences Biotechnology Cloning DNA Fingerprinting - methods DNA Primers - genetics DNA, Ribosomal - genetics Environmental Microbiology Enzymes Fundamental and applied biological sciences. Psychology Fungi - genetics Genes Life Sciences Microbial activity Microbial communities Microbial Genetics and Genomics Microbiological Techniques - methods Microbiology Mini-Review Multivariate statistics Noise Polymerase chain reaction Polymorphism Polymorphism, Restriction Fragment Length Ribonucleic acid RNA RNA, Ribosomal, 16S - genetics Statistical analysis Statistical methods Studies T-RFLP |
| 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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