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A Bifidobacterium mixed-species microarray for high resolution discrimination between intestinal bifidobacteria

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Author: Boesten, R.J. · Schuren, F.H.J. · Vos, W.M.de
Type:article
Date:2009
Institution: TNO Kwaliteit van Leven
Source:Journal of Microbiological Methods, 3, 76, 269-277
Identifier: 241428
doi: doi:10.1016/j.mimet.2008.12.006
Keywords: Biology · Biotechnology · Bifidobacterium · DNA-DNA hybridization · Genomic comparison · Microarray · bacterial DNA · RNA 16S · article · bacterial genome · bacterium identification · Bifidobacterium · Bifidobacterium adolescentis · Bifidobacterium animalis · Bifidobacterium bifidum · Bifidobacterium catenulatum · Bifidobacterium longum · Bifidobacterium pseudolongum · DNA DNA hybridization · DNA microarray · intestine flora · nonhuman · nucleotide sequence · priority journal · species identification · unindexed sequence · Animals · Bacterial Typing Techniques · Bifidobacterium · Cluster Analysis · Comparative Genomic Hybridization · DNA, Bacterial · Genome, Bacterial · Genomic Library · Intestines · Oligonucleotide Array Sequence Analysis · Phylogeny · RNA, Ribosomal, 16S · Species Specificity · Bifidobacterium · Bifidobacterium adolescentis · Bifidobacterium animalis · Bifidobacterium animalis subsp. animalis · Bifidobacterium animalis subsp. lactis · Bifidobacterium bifidum · Bifidobacterium catenulatum · Bifidobacterium longum · Bifidobacterium pseudolongum · Mammalia

Abstract

A genomic DNA-based microarray was constructed containing over 6000 randomly cloned genomic fragments of approximately 1-2 kb from six mammalian intestinal Bifidobacterium spp. including B. adolescentis, B. animalis, B. bifidum, B. catenulatum, B. longum and B. pseudolongum. This Bifidobacterium Mixed-Species (BMS) microarray was used to differentiate between type strains and isolates belonging to a set of nine Bifidobacterium spp. Hierarchical clustering of genomic hybridization data confirmed the grouping of the Bifidobacterium spp. according to the 16S rRNA-based phylogenetic clusters. In addition, these genomic hybridization experiments revealed high homology between the type-strain B. animalis subsp. lactis LMG18314 and B. animalis subsp. animalis LMG10508 (79%) as well as between the type strains B. longum biotype longum LMG13197 and B. longum biotype infantis LMG8811 (72%) - nevertheless, discrimination between these species was possible due to the high resolution output of the BMS-array. In addition, it was shown that the BMS-array could be used for assigning unknown Bifidobacterium isolates to a species group. Finally, a set of 54 diagnostic clones for Bifidobacterium identification was selected and sequenced to advance the understanding of the species-related differences. Remarkably, a large fraction (31%) of these was predicted to encode proteins that belong to the bifidobacterial glycobiome and another 11% had functional homology with genes involved in the protection against foreign DNA. Overall, the BMS-microarray is a high-resolution diagnostic tool that is able to facilitate the detection of strain- and species-specific characteristics of bifidobacteria. © 2008 Elsevier B.V. All rights reserved.