title: Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcus piscium MKFS47.
abstract: Lactococcus piscium is a psychrotrophic lactic acid bacterium and is known to be one of the predominant species within spoilage microbial communities in cold-stored packaged foods, particularly in meat products. Its presence in such products has been associated with the formation of buttery and sour off-odors. Nevertheless, the spoilage potential of L. piscium varies dramatically depending on the strain and growth conditions. Additional knowledge about the genome is required to explain such variation, understand its phylogeny, and study gene functions. Here, we present the complete and annotated genomic sequence of L. piscium MKFS47, combined with a time course analysis of the glucose catabolism-based transcriptome. In addition, a comparative analysis of gene contents was done for L. piscium MKFS47 and 29 other lactococci, revealing three distinct clades within the genus. The genome of L. piscium MKFS47 consists of one chromosome, carrying 2,289 genes, and two plasmids. A wide range of carbohydrates was predicted to be fermented, and growth on glycerol was observed. Both carbohydrate and glycerol catabolic pathways were significantly upregulated in the course of time as a result of glucose exhaustion. At the same time, differential expression of the pyruvate utilization pathways, implicated in the formation of spoilage substances, switched the metabolism toward a heterofermentative mode. In agreement with data from previous inoculation studies, L. piscium MKFS47 was identified as an efficient producer of buttery-odor compounds under aerobic conditions. Finally, genes and pathways that may contribute to increased survival in meat environments were considered.
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland margarita.andreevskaya@helsinki.fi.
authors.forename: Margarita
authors.initials: M
authors.lastname: Andreevskaya
authors.affiliation: Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
authors.forename: Per
authors.initials: P
authors.lastname: Johansson
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Pia
authors.initials: P
authors.lastname: Laine
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Olli-Pekka
authors.initials: OP
authors.lastname: Smolander
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Matti
authors.initials: M
authors.lastname: Sonck
authors.affiliation: Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
authors.forename: Riitta
authors.initials: R
authors.lastname: Rahkila
authors.affiliation: Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
authors.forename: Elina
authors.initials: E
authors.lastname: Jääskeläinen
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Lars
authors.initials: L
authors.lastname: Paulin
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Petri
authors.initials: P
authors.lastname: Auvinen
authors.affiliation: Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
authors.forename: Johanna
authors.initials: J
authors.lastname: Björkroth
mesh_terms: D001711:Biotransformation; D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D005285:Fermentation; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D005947:Glucose / Q000378:metabolism; D019344:Lactic Acid; D017045:Lactococcus / Q000235:genetics* / Q000254:growth & development; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008969:Molecular Sequence Data; D010957:Plasmids; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D019344:Lactic Acid; D005947:Glucose
references.citation: Methods Mol Biol. 2000;132:115-30
references.pmid: 10547834
references.citation: Mol Microbiol. 2013 Sep;89(6):1187-200
references.pmid: 23879596
references.citation: J Bacteriol. 2011 Jun;193(12):3000-8
references.pmid: 21498647
references.citation: Microbiol Immunol. 2007;51(9):889-92
references.pmid: 17895606
references.citation: Bioinformatics. 2015 May 15;31(10):1544-52
references.pmid: 25653249
references.citation: Nat Biotechnol. 2005 Dec;23(12):1527-33
references.pmid: 16273110
references.citation: PLoS One. 2011;6(8):e23184
references.pmid: 21829716
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W347-52
references.pmid: 21672955
references.citation: Int J Food Microbiol. 2007 Nov 1;119(3):340-5
references.pmid: 17913272
references.citation: Appl Environ Microbiol. 1980 Apr;39(4):926-7
references.pmid: 16345559
references.citation: Bioinformatics. 2010 Jan 1;26(1):139-40
references.pmid: 19910308
references.citation: Bioinformatics. 2013 Apr 15;29(8):1035-43
references.pmid: 23428641
references.citation: BMC Genomics. 2008;9:75
references.pmid: 18261238
references.citation: Infect Immun. 2011 Oct;79(10):4193-200
references.pmid: 21825065
references.citation: BMC Bioinformatics. 2003 Jun 3;4:21
references.pmid: 12783628
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: Int J Food Microbiol. 2013 Jul 1;165(1):43-50
references.pmid: 23688550
references.citation: Appl Environ Microbiol. 2008 Nov;74(22):6832-8
references.pmid: 18820069
references.citation: Int J Syst Evol Microbiol. 2008 Aug;58(Pt 8):1844-9
references.pmid: 18676466
references.citation: J Bacteriol. 1980 Oct;144(1):274-8
references.pmid: 6998951
references.citation: Meat Sci. 2010 Dec;86(4):889-95
references.pmid: 20800372
references.citation: Food Microbiol. 2009 Sep;26(6):638-44
references.pmid: 19527840
references.citation: Appl Environ Microbiol. 2014 Apr;80(7):2229-39
references.pmid: 24487531
references.citation: Food Microbiol. 2012 May;30(1):164-72
references.pmid: 22265297
references.citation: Microbiol Mol Biol Rev. 2012 Dec;76(4):740-72
references.pmid: 23204365
references.citation: Int J Food Microbiol. 2002 Sep 15;78(1-2):79-97
references.pmid: 12222639
references.citation: Int J Food Microbiol. 1996 Nov;33(1):103-20
references.pmid: 8913812
references.citation: FEMS Microbiol Lett. 1990 Mar 1;56(1-2):109-13
references.pmid: 1692000
references.citation: Appl Environ Microbiol. 1993 Jun;59(6):1893-7
references.pmid: 16348966
references.citation: Int J Food Microbiol. 2011 Jan 5;144(3):360-6
references.pmid: 21093087
references.citation: J Mol Microbiol Biotechnol. 2004;7(4):170-81
references.pmid: 15383715
references.citation: Antimicrob Agents Chemother. 2009 Apr;53(4):1598-609
references.pmid: 19164152
references.citation: Appl Environ Microbiol. 2002 Dec;68(12):6332-42
references.pmid: 12450858
references.citation: BMC Bioinformatics. 2010;11:119
references.pmid: 20211023
references.citation: Meat Sci. 2011 Jul;88(3):368-73
references.pmid: 21316866
references.citation: Appl Environ Microbiol. 2013 Feb;79(4):1078-85
references.pmid: 23204416
references.citation: Food Microbiol. 2014 May;39:61-7
references.pmid: 24387853
references.citation: J Bacteriol. 2012 Dec;194(23):6665
references.pmid: 23144409
references.citation: J Bacteriol. 2012 Nov;194(22):6364
references.pmid: 23105090
references.citation: FEMS Microbiol Lett. 2007 Nov;276(2):140-8
references.pmid: 17888009
references.citation: Stand Genomic Sci. 2011 Oct 15;5(1):168-93
references.pmid: 22180819
references.citation: Int J Food Microbiol. 2012 May 1;156(1):50-9
references.pmid: 22445914
references.citation: J Bioinform Comput Biol. 2008 Apr;6(2):387-401
references.pmid: 18464329
references.citation: Appl Environ Microbiol. 2011 Jul;77(13):4344-51
references.pmid: 21571876
references.citation: Int J Food Microbiol. 1996 Jul;30(3):293-302
references.pmid: 8854182
references.citation: Stand Genomic Sci. 2010 Jan 28;2(1):135-41
references.pmid: 21304685
references.citation: Int J Food Microbiol. 2013 Jan 1;160(3):227-38
references.pmid: 23290229
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W475-8
references.pmid: 21470960
references.citation: J Appl Microbiol. 2002;92(1):173-9
references.pmid: 11849342
references.citation: Curr Opin Microbiol. 1999 Apr;2(2):195-201
references.pmid: 10322165
references.citation: Food Microbiol. 2015 Feb;45(Pt A):83-102
references.pmid: 25481065
references.citation: J Appl Microbiol. 2008 Jan;104(1):171-7
references.pmid: 17850313
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W647-51
references.pmid: 20462861
references.citation: Mol Microbiol. 1994 Jun;12(5):737-45
references.pmid: 8052126
references.citation: Appl Environ Microbiol. 2015 Mar;81(6):1902-8
references.pmid: 25548057
references.citation: Lett Appl Microbiol. 2010 Apr;50(4):357-61
references.pmid: 20132434
references.citation: Int J Food Microbiol. 2014 May 16;178:120-9
references.pmid: 24690877
references.citation: J Bacteriol. 2012 Dec;194(24):6976-7
references.pmid: 23209230