Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria.
The genome-probing microarray (GPM) was developed for quantitative, high-throughput monitoring of community dynamics in lactic acid bacteria (LAB) fermentation through the deposit of 149 microbial genomes as probes on a glass slide. Compared to oligonucleotide microarrays, the specificity of GPM was remarkably increased to a species-specific level. GPM possesses about 10- to 100-fold higher sensitivity (2.5 ng of genomic DNA) than the currently used 50-mer oligonucleotide microarrays. Since signal variation between the different genomes was very low compared to that of cDNA or oligonucleotide-based microarrays, the capacity of global quantification of microbial genomes could also be observed in GPM hybridization. In order to assess the applicability of GPMs, LAB community dynamics were monitored during the fermentation of kimchi, a traditional Korean food. In this work, approximately 100 diverse LAB species could be quantitatively analyzed as actively involved in kimchi fermentation.
Bae
Jin-Woo
JW
Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Eundong 52, Yusong, Daejeon, South Korea.
Rhee
Sung-Keun
SK
Park
Ja Ryeong
JR
Chung
Won-Hyong
WH
Nam
Young-Do
YD
Lee
Insun
I
Kim
Hongik
H
Park
Yong-Ha
YH
D004269:DNA, Bacterial / Q000235:genetics* / Q000302:isolation & purification; D016680:Genome, Bacterial; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D007778:Lactobacillus / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny
D004269:DNA, Bacterial