Abstract
BackgroundPediococcus damnosus LMG 28219 is a lactic acid bacterium dominating the maturation phase of Flemish acid beer productions. It proved to be capable of growing in beer, thereby resisting this environment, which is unfavorable for microbial growth. The molecular mechanisms underlying its metabolic capabilities and niche adaptations were unknown up to now. In the present study, whole-genome sequencing and comparative genome analysis were used to investigate this strain’s mechanisms to reside in the beer niche, with special focus on not only stress and hop resistances but also folate biosynthesis and exopolysaccharide (EPS) production.ResultsThe draft genome sequence of P. damnosus LMG 28219 harbored 183 contigs, including an intact prophage region and several coding sequences involved in plasmid replication. The annotation of 2178 coding sequences revealed the presence of many transporters and transcriptional regulators and several genes involved in oxidative stress response, hop resistance, de novo folate biosynthesis, and EPS production. Comparative genome analysis of P. damnosus LMG 28219 with Pediococcus claussenii ATCC BAA-344T (beer origin) and Pediococcus pentosaceus ATCC 25745 (plant origin) revealed that various hop resistance genes and genes involved in de novo folate biosynthesis were unique to the strains isolated from beer. This contrasted with the genes related to osmotic stress responses, which were shared between the strains compared. Furthermore, transcriptional regulators were enriched in the genomes of bacteria capable of growth in beer, suggesting that those cause rapid up- or down-regulation of gene expression.ConclusionsGenome sequence analysis of P. damnosus LMG 28219 provided insights into the underlying mechanisms of its adaptation to the beer niche. The results presented will enable analysis of the transcriptome and proteome of P. damnosus LMG 28219, which will result in additional knowledge on its metabolic activities.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1438-z) contains supplementary material, which is available to authorized users.
Highlights
Pediococcus damnosus LMG 28219 is a lactic acid bacterium dominating the maturation phase of Flemish acid beer productions
Draft genome sequences are available for several strains of Pediococcus acidilactici, namely strain MA 18/5 M originating from animal food, strain DSM 20284 isolated from barley, strain 7_4 from a human fecal sample, and strain NGRI 0510Q, formerly known as Pediococcus lolii [18], isolated from ryegrass silage
General architecture and annotation of the Pediococcus damnosus LMG 28219 draft genome Paired-end sequencing of the P. damnosus LMG 28219 genomic DNA yielded 3,137,316 reads that were assembled into 183 contigs [N50 of 24,659 base pairs], consisting of 69 large (>10,000 nucleotides) and 114 small (
Summary
Pediococcus damnosus LMG 28219 is a lactic acid bacterium dominating the maturation phase of Flemish acid beer productions It proved to be capable of growing in beer, thereby resisting this environment, which is unfavorable for microbial growth. Beer is a fermented beverage that is high in ethanol, carbon dioxide and flavorful yeast metabolites, contains hopderived flavor and antimicrobial compounds, and is low in pH, oxygen, and residual nutrients [1] This environment has selected for unique groups of bacteria specialized in growth in beer, including several species of lactic acid bacteria (LAB). Pediococcus species possess rather small genomes (approximately 2 Mb), encoding a broad repertoire of transporters for efficient carbon and nitrogen acquisition and reflecting a limited range of biosynthetic capabilities. Several strains possess plasmids containing genes regulating the fermentation of carbohydrates and encoding different types of resistances (e. g., resistance to stress, hop, or antibiotics) [17,19]
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