Comparative genome analysis of Pediococcus damnosus LMG 28219, a strain well-adapted to the beer environment

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.

Microbial acidification, alcoholization, and aroma production during spontaneous lambic beer production

“…brevis and P. damnosus are commonly found beer spoilage microorganisms . They are, like some other LAB species, well adapted to growth in beer, thanks to a plasmid‐encoded transporter protein HorA and a multi‐drug transporter ORF5, which transport the hop antimicrobial compounds out of the cytoplasm . Transcriptome analysis of a beer‐spoiling Lb.…”

“…The most commonly isolated LAB species, of which the growth coincides with the summer months of the lambic beer production process, is P. damnosus (previously identified as Pediococcus cerevisiae ), which is a homofermentative LAB species, thereby producing only lactate by reducing pyruvate for NAD + recuperation by means of a lactate dehydrogenase enzyme (Fig. ) . When wort is acidified beforehand, the acidification and maturation phases overlap and, hence, they can be regarded as one single long maturation phase .…”

“…90 They are, like some other LAB species, well adapted to growth in beer, thanks to a plasmid-encoded transporter protein HorA and a multi-drug transporter ORF5, which transport the hop antimicrobial compounds out of the cytoplasm. [91][92][93][94] Transcriptome analysis of a beer-spoiling Lb. brevis strain has indeed shown that plasmid transcription is important for growth in both gassed and degassed beers.…”

“…3). 15,40,42,66,92 When wort is acidified beforehand, the acidification and maturation phases overlap and, hence, they can be regarded as one single long maturation phase. 42 Lactic acid bacteria are also part of the core microbiota in other spontaneously fermented acidic beers, such as ACAs and red-brown acidic ales.…”

“…42 Lactic acid bacteria are also part of the core microbiota in other spontaneously fermented acidic beers, such as ACAs and red-brown acidic ales. 29,30,40,92 Acetic acid bacteria Together with the LAB, a (variable) increase in AAB occurs during lambic beer production (Fig. 2), which can be undesirable, as excessive AAB growth leads to extensive acidification, creating an undesirable flavor profile in lambic beers.…”