Oligonucleotide microarrays for the detection and identification of viable beer spoilage bacteria

Abstract

Aims: The design and evaluation of an oligonucleotide microarray in order to detect and identify viable bacterial species that play a significant role in beer spoilage. These belong to the species of the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus. Methods and Results: Oligonucleotide probes specific to beer spoilage bacteria were designed. In order to detect viable bacteria, the probes were designed to target the intergenic spacer regions (ISR) between 16S and 23S rRNA. Prior to hybridization the ISR were amplified by combining reverse transcriptase and polymerase chain reactions using a designed consenus primer. The developed oligonucleotide microarrays allows the detection of viable beer spoilage bacteria. Conclusions: This method allows the detection and discrimination of single bacterial species in a sample containing complex microbial community. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non growing bacteria. Significance and Impact of the Study: The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage micro‐organisms within a mixed population.

Community Dynamics of Bacteria in Sourdough Fermentations as Revealed by Their Metatranscriptome

“…To be able to identify members of bacterial ecosystems in a broad and high-throughput way, several microarrays have been developed recently (1,22,26,34,35,37). Actually, two types of microarrays can be distinguished: (i) microarrays that contain partial 16S rRNA gene sequences as targets, also referred to as phylogenetic oligonucleotide microarrays; and (ii) microarrays that contain integral genomic DNA as targets, also referred to as community genome microarrays (38).…”

Nucleic acid detection technologies and marker molecules in bacterial diagnostics

“…Examples include conventional PCR [44], multiplex PCR [45], multiplex PCR with culture enrichment [46] and reversetranscriptase PCR for RNA targets [47]. From the available isothermal amplification technologies, NASBA has been described in combination with microarray detection [36,48].…”

Improved Enrichment Cultivation of Beer Spoiling Lactic Acid Bacteria by Continuous Glucose Addition to the Culture

“…The long adaptation time needed in the beginning of the enrichment cultivation can result in detection delay by several days. In order to shorten the detection time, several molecular methods have been developed for the detection of beer spoiling LAB, based on techniques such as microarrays 20 , PCR 10,16,23 , immunoassays [21][22] , riboprinting 4 , and RNA sandwich hybridization 11 .…”