A Bifidobacterium mixed-species microarray for high resolution discrimination between intestinal bifidobacteria.
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.
Boesten
Rolf J
RJ
Microbiology Department, TNO Quality of Life, Zeist, The Netherlands. r.boesten@cbs.knaw.nl <r.boesten@cbs.knaw.nl>
Schuren
Frank H J
FH
de Vos
Willem M
WM
D000818:Animals; D015373:Bacterial Typing Techniques; D001644:Bifidobacterium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D015698:Genomic Library; D007422:Intestines / Q000382:microbiology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013045:Species Specificity
D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S