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Zurich Open Repository and Archive 

Permanent URL to this publication: http://dx.doi.org/10.5167/uzh-9820

Schönmann, S; Loy, A; Wimmersberger, C; Sobek, J; Aquino, C; Vandamme, P; Frey, B; Rehrauer, H; Eberl, L (2009). 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia. Environmental Microbiology, 11(4):779-800.

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Abstract

For cultivation-independent and highly parallel analysis of members of the genus Burkholderia, an oligonucleotide microarray (phylochip) consisting of 131 hierarchically nested 16S rRNA gene-targeted oligonucleotide probes was developed. A novel primer pair was designed for selective amplification of a 1.3 kb 16S rRNA gene fragment of Burkholderia species prior to microarray analysis. The diagnostic performance of the microarray for identification and differentiation of Burkholderia species was tested with 44 reference strains of the genera Burkholderia, Pandoraea, Ralstonia and Limnobacter. Hybridization patterns based on presence/absence of probe signals were interpreted semi-automatically using the novel likelihood-based strategy of the web-tool Phylo- Detect. Eighty-eight per cent of the reference strains were correctly identified at the species level. The evaluated microarray was applied to investigate shifts in the Burkholderia community structure in acidic forest soil upon addition of cadmium, a condition that selected for Burkholderia species. The microarray results were in agreement with those obtained from phylogenetic analysis of Burkholderia 16S rRNA gene sequences recovered from the same cadmiumcontaminated soil, demonstrating the value of the Burkholderia phylochip for determinative and environmental studies.

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
07 Faculty of Science > Institute of Plant Biology
08 University Research Priority Programs > Systems Biology / Functional Genomics
DDC:570 Life sciences; biology
580 Plants (Botany)
610 Medicine & health
Language:English
Date:September 2009
Deposited On:14 Jan 2009 15:49
Last Modified:27 Nov 2013 20:57
Publisher:Wiley-Blackwell
ISSN:1462-2912
Additional Information:Free access at DOI
Publisher DOI:10.1111/j.1462-2920.2008.01800.x
PubMed ID:19396938
Citations:Web of Science®. Times Cited: 9
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Scopus®. Citation Count: 9

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