Weckx Stefan, Allemeersch Joke, Van der Meulen Roel, Vrancken Gino, Huys Geert, Vandamme Peter, Van Hummelen Paul, De Vuyst Luc
Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
Appl Environ Microbiol. 2009 Oct;75(20):6488-95. doi: 10.1128/AEM.01055-09. Epub 2009 Aug 14.
During the last few years, genome-related information has become available for many microorganisms, including important food-related bacteria. Lactic acid bacteria (LAB) are important industrially in the production of fermented foods such as dairy products, sausages, sourdoughs, and vegetables. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as flavor and texture. In the present study, a species-independent functional gene microarray was developed that targets 406 genes that play key roles in the production of sugar catabolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in the stress response. Also, genes linked to negative traits, such as antibiotic resistance and virulence, are represented. As LAB ecosystems contain a variety of species, there was a more global focus on these specific functional properties. Thus, an algorithm was used to design gene-specific oligonucleotides that preferably hybridize with multiple LAB species, thereby allowing controlled cross-hybridization. For proof of concept, the microarray composed of 2,269 30-mer oligonucleotides focused on LAB species that are prevalent in sourdough ecosystems. Validation hybridizations using DNA and RNA from 18 LAB strains, covering 86% of all the oligonucleotides, showed that there were wide ranges in intensity and high reproducibility between microarrays.
在过去几年中，已经获得了许多微生物的基因组相关信息，包括与食品相关的重要细菌。乳酸菌（LAB）在工业上对发酵食品（如乳制品、香肠、酸面团和蔬菜）的生产非常重要。尽管乳酸菌的代谢能力有限，但它们对发酵食品的重要特性（如风味和质地）有很大贡献。在本研究中，开发了一种不依赖物种的功能基因微阵列，该阵列靶向406个基因，这些基因在糖分解代谢产物、细菌素、胞外多糖和香气的产生、益生菌和生物安全特性以及应激反应中起关键作用。此外，还包括与抗生素抗性和毒力等负面特征相关的基因。由于乳酸菌生态系统包含多种物种，因此更全面地关注这些特定的功能特性。因此，使用一种算法来设计基因特异性寡核苷酸，这些寡核苷酸最好能与多种乳酸菌物种杂交，从而实现可控的交叉杂交。为了验证概念，由2269个30聚体寡核苷酸组成的微阵列聚焦于酸面团生态系统中普遍存在的乳酸菌物种。使用来自18株乳酸菌菌株的DNA和RNA进行的验证杂交覆盖了所有寡核苷酸的86%，结果表明微阵列之间的强度范围很广且重现性高。
