title: Development and validation of a species-independent functional gene microarray that targets lactic acid bacteria.
abstract: 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.
authors.affiliation: 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. stefan.weckx@vub.ac.be
authors.forename: Stefan
authors.initials: S
authors.lastname: Weckx
authors.forename: Joke
authors.initials: J
authors.lastname: Allemeersch
authors.forename: Roel
authors.initials: R
authors.lastname: Van der Meulen
authors.forename: Gino
authors.initials: G
authors.lastname: Vrancken
authors.forename: Geert
authors.initials: G
authors.lastname: Huys
authors.forename: Peter
authors.initials: P
authors.lastname: Vandamme
authors.forename: Paul
authors.initials: P
authors.lastname: Van Hummelen
authors.forename: Luc
authors.initials: L
authors.lastname: De Vuyst
mesh_terms: D000465:Algorithms; D017753:Ecosystem; D005285:Fermentation; D005516:Food Microbiology; D005798:Genes, Bacterial; D007778:Lactobacillus / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D015203:Reproducibility of Results; D013045:Species Specificity
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