title: Genomic comparison of sporeforming bacilli isolated from milk.
abstract: BACKGROUND
  Sporeformers in the order Bacillales are important contributors to spoilage of pasteurized milk. While only a few Bacillus and Viridibacillus strains can grow in milk at 6°C, the majority of Paenibacillus isolated from pasteurized fluid milk can grow under these conditions. To gain a better understanding of genomic features of these important spoilage organisms and to identify candidate genomic features that may facilitate cold growth in milk, we performed a comparative genomic analysis of selected dairy associated sporeformers representing isolates that can and cannot grow in milk at 6°C.
  
  
  RESULTS
  The genomes for seven Paenibacillus spp., two Bacillus spp., and one Viridibacillus sp. isolates were sequenced. Across the genomes sequenced, we identified numerous genes encoding antimicrobial resistance mechanisms, bacteriocins, and pathways for synthesis of non-ribosomal peptide antibiotics. Phylogenetic analysis placed genomes representing Bacillus, Paenibacillus and Viridibacillus into three distinct well supported clades and further classified the Paenibacillus strains characterized here into three distinct clades, including (i) clade I, which contains one strain able to grow at 6°C in skim milk broth and one strain not able to grow under these conditions, (ii) clade II, which contains three strains able to grow at 6°C in skim milk broth, and (iii) clade III, which contains two strains unable to grow under these conditions. While all Paenibacillus genomes were found to include multiple copies of genes encoding β-galactosidases, clade II strains showed significantly higher numbers of genes encoding these enzymes as compared to clade III strains. Genome comparison of strains able to grow at 6°C and strains unable to grow at this temperature identified numerous genes encoding features that might facilitate the growth of Paenibacillus in milk at 6°C, including peptidases with cold-adapted features (flexibility and disorder regions in the protein structure) and cold-adaptation related proteins (DEAD-box helicases, chaperone DnaJ).
  
  
  CONCLUSIONS
  Through a comparative genomics approach we identified a number of genomic features that may relate to the ability of selected Paenibacillus strains to cause spoilage of refrigerated fluid milk. With additional experimental evidence, these data will facilitate identification of targets to detect and control Gram positive spore formers in fluid milk.
authors.forename: Andrea I
authors.initials: AI
authors.lastname: Moreno Switt
authors.forename: Alexis D
authors.initials: AD
authors.lastname: Andrus
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Ranieri
authors.forename: Renato H
authors.initials: RH
authors.lastname: Orsi
authors.forename: Reid
authors.initials: R
authors.lastname: Ivy
authors.forename: Henk C
authors.initials: HC
authors.lastname: den Bakker
authors.forename: Nicole H
authors.initials: NH
authors.lastname: Martin
authors.forename: Martin
authors.initials: M
authors.lastname: Wiedmann
authors.affiliation: 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA. kjb4@cornell.edu.
authors.forename: Kathryn J
authors.initials: KJ
authors.lastname: Boor
mesh_terms: D000818:Animals; D023181:Antimicrobial Cationic Peptides / Q000096:biosynthesis; D001407:Bacillus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001430:Bacteriocins / Q000235:genetics / Q000378:metabolism; D002417:Cattle; D053487:DEAD-box RNA Helicases / Q000235:genetics / Q000378:metabolism; D024881:Drug Resistance, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D050956:HSP40 Heat-Shock Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D008892:Milk / Q000382:microbiology*; D056507:Paenibacillus / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D010641:Phenotype; D010802:Phylogeny; D013171:Spores, Bacterial / Q000235:genetics / Q000378:metabolism; D001616:beta-Galactosidase / Q000235:genetics / Q000378:metabolism
chemical_list: D023181:Antimicrobial Cationic Peptides; D001426:Bacterial Proteins; D001430:Bacteriocins; D050956:HSP40 Heat-Shock Proteins; D001616:beta-Galactosidase; D053487:DEAD-box RNA Helicases