Boesten Rolf J, Schuren Frank H J, de Vos Willem M
Microbiology Department, TNO Quality of Life, Zeist, The Netherlands.
J Microbiol Methods. 2009 Mar;76(3):269-77. doi: 10.1016/j.mimet.2008.12.006. Epub 2008 Dec 24.
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.
构建了基于基因组DNA的微阵列，其包含来自六种哺乳动物肠道双歧杆菌属（包括青春双歧杆菌、动物双歧杆菌、两歧双歧杆菌、链状双歧杆菌、长双歧杆菌和假长双歧杆菌）的6000多个随机克隆的约1 - 2 kb基因组片段。该双歧杆菌混合种（BMS）微阵列用于区分属于九种双歧杆菌属的模式菌株和分离株。基因组杂交数据的层次聚类证实了双歧杆菌属根据基于16S rRNA的系统发育簇进行的分组。此外，这些基因组杂交实验揭示了模式菌株动物双歧杆菌乳酸亚种LMG18314和动物双歧杆菌动物亚种LMG10508之间的高度同源性（79%），以及模式菌株长双歧杆菌长亚种LMG13197和长双歧杆菌婴儿亚种LMG8811之间的高度同源性（72%）——然而，由于BMS阵列的高分辨率输出，仍可区分这些物种。此外，研究表明BMS阵列可用于将未知的双歧杆菌分离株归为一个物种组。最后，选择并测序了一组54个用于双歧杆菌鉴定的诊断克隆，以增进对物种相关差异的理解。值得注意的是，其中很大一部分（31%）预计编码属于双歧杆菌糖生物学组的蛋白质，另有11%与参与抵御外源DNA的基因具有功能同源性。总体而言，BMS微阵列是一种高分辨率诊断工具，能够促进双歧杆菌菌株和物种特异性特征的检测。
