Metatranscriptome analysis of lactic acid bacteria during kimchi fermentation with genome-probing microarrays

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Title
Metatranscriptome analysis of lactic acid bacteria during kimchi fermentation with genome-probing microarrays
Author(s)
Young-Do Nam; H W Jang; K H Kim; Sung Un No; Jin-Woo Bae
Bibliographic Citation
International Journal of Food Microbiology, vol. 130, no. 2, pp. 140-146
Publication Year
2009
Abstract
We constructed genome probing microarrays (GPM) that are specific to 39 lactic acid bacteria (LAB) in an effort to monitor microbial diversity and biological activity during the fermentation of kimchi, a traditional Korean vegetable product known to contain various health-promoting and immunity-boosting factors. Metagenomes and metatranscriptomes extracted from periodically sampled kimchi soup were labeled, hybridized and comparatively analyzed using GPMs. Each metatranscriptome was prepared by subtracting 16S rRNA and 23S rRNA from the total RNA, and selectively synthesizing mRNA-specific cDNAs from the rRNA-subtracted samples. Metagenomic analysis revealed 23 LAB related to kimchi fermentation [defined as bacteria with more than a 1% average relative composition (ARC)]. Metatranscriptome analysis revealed that, with the exception of two microorganisms, all LAB probed in the microarray contributed to kimchi fermentation. Moreover, the relative compositions of the major LAB remained unchanged (there was less than a 1.5% difference between the maximum and minimum values) in our metagenome analysis, while our metatranscriptome analysis revealed significant differences in the relative compositions of major LAB during fermentation (relative compositions changed by 2.4% to 9.5%). These data indicate that microorganisms that are less abundant in the flora (those with less than a 5% ARC in the metagenomic analysis) also participated in kimchi fermentation with relatively high activities.
Keyword
GPMkimchilactic acid bacteriametagenomemetatranscriptome
ISSN
0168-1605
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.ijfoodmicro.2009.01.007
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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