Coupling of denaturing high-performance liquid chromatography and terminal restriction fragment length polymorphism with precise fragment sizing for microbial community profiling and characterization. - CNRS - Centre national de la recherche scientifique Accéder directement au contenu
Article Dans Une Revue Applied and Environmental Microbiology Année : 2010

Coupling of denaturing high-performance liquid chromatography and terminal restriction fragment length polymorphism with precise fragment sizing for microbial community profiling and characterization.

Résumé

Terminal restriction fragment length polymorphism (T-RFLP) is used to monitor the structural diversity of complex microbial communities in terms of richness, relative abundance, and distribution of the major subpopulations and individual members. However, discrepancies of several nucleotides between expected and experimentally observed lengths of terminal restriction fragments (T-RFs), together with the difficulty of obtaining DNA sequence information from T-RFLP profiling, often prevent accurate phylogenetic characterization of the microbial community of interest. In this study, T-RFLP analysis of DNA from an artificial assembly of five bacterial strains was carried out with a combination of two size markers with different fluorescent tags. Precise sizing of T-RFs in the 50- to 500-nucleotide range was achieved by using the same dye for both samples and size markers. Phylogenetic assignment of the component microbial strains was facilitated by coupling T-RFLP to denaturing high-performance liquid chromatography (D-HPLC) of 16S RNA gene fragments followed by direct sequencing. The proposed coupling of D-HPLC and T-RFLP provides unambiguous characterization of microbial communities containing less than 15 microbial strains.

Dates et versions

hal-00454252 , version 1 (08-02-2010)

Identifiants

Citer

Christian Penny, Thierry Nadalig, Malek Alioua, Christelle Gruffaz, Stéphane Vuilleumier, et al.. Coupling of denaturing high-performance liquid chromatography and terminal restriction fragment length polymorphism with precise fragment sizing for microbial community profiling and characterization.. Applied and Environmental Microbiology, 2010, 76 (3), pp.648-51. ⟨10.1128/AEM.01556-09⟩. ⟨hal-00454252⟩
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