title: Comparative genome analysis of Pediococcus damnosus LMG 28219, a strain well-adapted to the beer environment.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  The 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-344(T) (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.
  
  
  CONCLUSIONS
  Genome 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.
authors.affiliation: Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium. isabel.snauwaert@ugent.be.
authors.forename: Isabel
authors.initials: I
authors.lastname: Snauwaert
authors.affiliation: Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium. Pieter.Stragier@ugent.be.
authors.forename: Pieter
authors.initials: P
authors.lastname: Stragier
authors.affiliation: Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium. ldvuyst@vub.ac.be.
authors.forename: Luc
authors.initials: L
authors.lastname: De Vuyst
authors.affiliation: Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium. Peter.Vandamme@ugent.be.
authors.forename: Peter
authors.initials: P
authors.lastname: Vandamme
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001515:Beer / Q000382:microbiology*; D055028:Comparative Genomic Hybridization; D005492:Folic Acid / Q000096:biosynthesis; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D018384:Oxidative Stress / Q000235:genetics; D010376:Pediococcus / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D010957:Plasmids / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D005492:Folic Acid