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Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities

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dc.contributor.authorBlackwood, Christopher B., author
dc.contributor.authorMarsh, Terry, author
dc.contributor.authorKim, Sang-Hoon, author
dc.contributor.authorPaul, Eldor A., author
dc.contributor.authorAmerican Society for Microbiology, publisher
dc.date.accessioned2007-01-03T06:06:38Z
dc.date.available2007-01-03T06:06:38Z
dc.date.issued2003-02
dc.description.abstractTerminal restriction fragment length polymorphism (T-RFLP) is a culture-independent method of obtaining a genetic fingerprint of the composition of a microbial community. Comparisons of the utility of different methods of (i) including peaks, (ii) computing the difference (or distance) between profiles, and (iii) performing statistical analysis were made by using replicated profiles of eubacterial communities. These samples included soil collected from three regions of the United States, soil fractions derived from three agronomic field treatments, soil samples taken from within one meter of each other in an alfalfa field, and replicate laboratory bioreactors. Cluster analysis by Ward's method and by the unweighted-pair group method using arithmetic averages (UPGMA) were compared. Ward's method was more effective at differentiating major groups within sets of profiles; UPGMA had a slightly reduced error rate in clustering of replicate profiles and was more sensitive to outliers. Most replicate profiles were clustered together when relative peak height or Hellinger-transformed peak height was used, in contrast to raw peak height. Redundancy analysis was more effective than cluster analysis at detecting differences between similar samples. Redundancy analysis using Hellinger distance was more sensitive than that using Euclidean distance between relative peak height profiles. Analysis of Jaccard distance between profiles, which considers only the presence or absence of a terminal restriction fragment, was the most sensitive in redundancy analysis, and was equally sensitive in cluster analysis, if all profiles had cumulative peak heights greater than 10,000 fluorescence units. It is concluded that T-RFLP is a sensitive method of differentiating between microbial communities when the optimal statistical method is used for the situation at hand. It is recommended that hypothesis testing be performed by redundancy analysis of Hellinger-transformed data and that exploratory data analysis be performed by cluster analysis using Ward's method to find natural groups or by UPGMA to identify potential outliers. Analyses can also be based on Jaccard distance if all profiles have cumulative peak heights greater than 10,000 fluorescence units.
dc.format.mediumborn digital
dc.format.mediumarticles
dc.identifier.bibliographicCitationBlackwood, Christopher B., Terry Marsh, Sang-Hoon Kim, and Eldor A. Paul, Terminal Restriction Fragment Length Polymorphism Data Analysis for Quantitative Comparison of Microbial Communities. Applied and Environmental Microbiology 69 no. 2 (February 2003): 926-932. https://dx.doi.org/10.1128/AEM.69.2.926-932.2003.
dc.identifier.doihttps://dx.doi.org/10.1128/AEM.69.2.926-932.2003
dc.identifier.urihttp://hdl.handle.net/10217/80863
dc.languageEnglish
dc.language.isoeng
dc.publisherColorado State University. Libraries
dc.relation.ispartofFaculty Publications
dc.rights©2003 American Society for Microbiology.
dc.rightsCopyright and other restrictions may apply. User is responsible for compliance with all applicable laws. For information about copyright law, please see https://libguides.colostate.edu/copyright.
dc.subjectenvironmental samples
dc.subjectfluorescence baseline
dc.subjectstatistical analysis
dc.subjectmolecular genetic technique
dc.titleTerminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities
dc.typeText

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