New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities.

ABSTRACT: Terminal restriction fragment length polymorphism (T-RFLP) analysis has the potential to be useful for comparisons of complex bacterial communities, especially to detect changes in community structure in response to different variables. To do this successfully, systematic variations have to be detected above method-associated noise, by standardizing data sets and assigning confidence estimates to relationships detected. We investigated the use of different standardizing methods in T-RFLP analysis of PCR-amplified 16S rRNA genes to elucidate the similarities between the bacterial communities in 17 soil and sediment samples. We developed a robust method for standardizing data sets that appeared to allow detection of similarities between complex bacterial communities. We term this the variabl

SUBMITTER: Osborne CA 

PROVIDER: S-EPMC1392978 | biostudies-literature | 2006 Feb

REPOSITORIES: biostudies-literature