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Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences
- Kisand, Veljo (author)
-
- Wikner, Johan, 1961- (author)
- Umeå universitet,Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet),Johan Wikner
- (creator_code:org_t)
- 2003
- 2003
- English.
- In: Journal of Microbiological Methods. - 0167-7012 .- 1872-8359. ; 54:2, s. 183-191
- Journal article (peer-reviewed)
Abstract
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- The phylogenetic affiliation of 91 operational taxonomic units, randomly sampled from three aquatic microcosm experiments, was investigated by two PCR based and one culture dependent method. The occurrence of multiple melting domains and poor coupling between Tin and DGGE retardation was demonstrated to cause poor resolution at the species level in PCR-DGGE analysis of microbial communities. We also showed that the problem of multiple melting domains was particularly prone for brackish water bacterioplankton in the Flavobacterium genus, providing characteristic band morphology for this genus. Banding patterns from DGGE analysis may therefore be misinterpreted in terms of the species richness in natural bacterial communities, when using commonly applied universal primers. (C) 2003 Elsevier Science B.V. All rights reserved.
Subject headings
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
Keyword
- 16S rDNA
- flavobacteria
- melting temperature
- multiple melting domains
- PCR-DGGE
- phylogeny
Publication and Content Type
- ref (subject category)
- art (subject category)
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