Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics

International Journal of Food Microbiology

Volumn 157, Issue 2, 2012, Pages 142-149

  Nieminen, T T ^a   Koskinen, K ^b   Laine, P ^b   Hultman, J ^a,b   Sade E ^a   Paulin, L ^b   Paloranta, A ^a   Johansson, P ^a   Bjorkroth J ^a   Auvinen, P ^b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Lactic acid bacteria; Meat; Metagenomics; Spoilage

Indexed keywords

ACETIC ACID; LACTIC ACID; OIL; RNA 16S; SUGAR;

AMPLICON; ARTICLE; BACTERIUM COLONY; BACTERIUM IDENTIFICATION; BROCHOTHRIX THERMOSPHACTA; BROILER; CARBOHYDRATE METABOLISM; CARNOBACTERIUM; CHICKEN MEAT; CLOSTRIDIUM; COMPARATIVE STUDY; DNA SEQUENCE; ENTEROBACTERIACEAE; FOOD PRESERVATION; FOOD PROCESSING; FOOD SPOILAGE; GENE SEQUENCE; LACTOBACILLUS; LEUCONOSTOC; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; POULTRY; RNA GENE; SHELF LIFE; SPICE; VIBRIO;

ANIMALS; BACTERIA; CARNOBACTERIUM; COLONY COUNT, MICROBIAL; DNA, BACTERIAL; FINLAND; FOOD MICROBIOLOGY; FOOD PACKAGING; FOOD PRESERVATION; LEUCONOSTOC; MEAT; METAGENOMICS; POULTRY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); BROCHOTHRIX; CARNOBACTERIUM; CLOSTRIDIUM; ENTEROBACTERIACEAE; LACTOBACILLUS; LEUCONOSTOC; LEUCONOSTOC GASICOMITATUM; LEUCONOSTOC GELIDUM; VAGOCOCCUS; VIBRIO;

EID: 84862874448     PISSN: 01681605     EISSN: 18793460     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2012.04.016     Document Type: Article

References (44)

1. Bentley D. Whole-genome re-sequencing. Current Opinion in Genetics and Development 2006, 16:545-552.
2. Björkroth J. Microbiological ecology of marinated meat products. Meat Science 2005, 70:477-480.
3. Björkroth J., Geisen R., Schillinger U., Weiss N., De Vos P., Holzapfel W., Korkeala H., Vandamme P. Characterization of Leuconostoc gasicomitatum sp. nov., associated with spoiled raw tomato-marinated broiler meat strips packaged under modified-atmosphere conditions. Applied and Environmental Microbiology 2000, 66:3764-3772.
4. Björkroth K.J., Schillinger U., Geisen R., Weiss N., Holzapfel W.H., Korkeala H.J., Hoste B., Vandamme P. Taxonomic study of Weissella confusa and description of Weissella cibaria sp. nov., a novel species detected in food and clinical samples. International Journal of Systematic and Evolutionary Microbiology 2002, 52:141-148.
5. Borch E., Kant-Muermans M.L., Blixt Y. Bacterial spoilage of meat and cured meat products. International Journal of Food Microbiology 1996, 33:103-120.
6. Cambon-Bonavita M., Lesongeur F., Menoux S., Lebourg A., Barbier G. Microbial diversity in smoked salmon examined by a culture-independent molecular approach-a preliminary study. International Journal of Food Microbiology 2001, 70:179-187.
7. Dalgaard P., Mejlholm O., Christiansen T., Huss H. Importance of Photobacterium phosphoreum in relation to spoilage of modified atmosphere-packed fish products. Letters in Applied Microbiology 1997, 24:373-378.
8. Devlieghere F., Vermeiren L., Bontenbal E., Lamers P.-P., Debevere J. Reducing salt intake from meat products by combined use of lactate and diacetate salts without affecting microbial stability. International Journal of Food Science and Technology 2009, 44:337-341.
9. Edwards U., Rogall T., Blocker H., Emde M., Bottger E. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Research 1989, 17:7843-7853.
10. Ercolini D., Ferrocino I., Nasi A., Ndagijimana M., Vernocchi P., La Storia A., Laghi A., Mauriello G., Guerzoni M.E., Villani F. Microbial metabolites and bacterial diversity in beef stored in different packaging conditions monitored by pyrosequencing, PCR-DGGE, SPME-GC/MS and HNMR. Applied and Environmental Microbiology 2011, 10.1128/AEM.05521-11.
11. González-Rodríguez M., Sanz J., Santos J., Otero A., García-López M. Numbers and types of microorganisms in vacuum-packed cold-smoked freshwater fish at the retail level. International Journal of Food Microbiology 2002, 77:161-168.
12. Haas B., Gevers D., Ashlee M., Feldgarden M., Ward D., Giannoukos G., Ciulla D., Tabbaa D., Highlander S., Sodergren E., Methé B., DeSantis T., Human Microbiome Consortium, Petrosino J., Knight R., Birren B. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research 2011, 21:494-504.
13. Handelsman J., Rondon M., Brady S., Clardy J., Goodman R. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemical Biology 1998, 5:R245-R249.
14. Hoyles L., Lawson P., Foster G., Falsen E., Ohlen M., Grainger J., Collins M. Vagococcus fessus sp. nov., isolated from a seal and a harbour porpoise. International Journal of Systematic and Evolutionary Microbiology 2000, 50:1151-1154.
15. Huse S., Welch D., Morrison H., Sogin M. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology 2010, 12:1889-1898.
16. Huson D., Auch A., Qi J., Schuster S. MEGAN analysis of metagenomic data. Genome Research 2007, 17:377-386.
17. Joffraud J., Cardinal M., Cornet J., Chasles J., Léon S., Gigout F., Leroi F. Effect of bacterial interactions on the spoilage of cold-smoked salmon. International Journal of Food Microbiology 2006, 112:51-61.
18. T, in association with specific spoilage reactions. Applied and Environmental Microbiology 2011, 77:4344-4351.
19. Jung J., Lee S., Kim J., Park M., Bae J.-W., Hahn Y., Madsen E., Jeon C. Metagenomic analysis of Kimchi, the Korean traditional fermented food. Applied and Environmental Microbiology 2011, 77:2264-2274.
20. Kakouri A., Nychas G.J. Storage of poultry meat under modified atmospheres or vacuum packs: possible role of microbial metabolites as indicator of spoilage. Journal of Applied Bacteriology 1994, 76:163-172.
21. Kalinowski R.M., Tompkin R.B. Psychrotrophic clostridia causing spoilage in cooked meat and poultry products. Journal of Food Protection 1999, 62:766-772.
22. Koort J., Murros A., Coenye T., Eerola S., Vandamme P., Sukura A., Björkroth J. Lactobacillus oligofermentans sp. nov., associated with spoilage of modified-atmosphere-packaged poultry products. Applied and Environmental Microbiology 2005, 71:4400-4406.
23. Korkeala H., Alanko T., Mäkelä P., Lindroth S. Shelf-life of vacuum-packed cooked ring sausages at different chill temperatures. International Journal of Food Microbiology 1989, 9:237-247.
24. Koskinen K., Hultman J., Paulin L., Auvinen P., Kankaanpää H. Spatially differing bacterial communities in water columns of the northern Baltic Sea. FEMS Microbiology Ecology 2011, 75:99-110.
25. Leisner J.J., Laursen B., Provost H., Drider D., Dalgaard P. Carnobacterium: positive and negative effects in the environment and in foods. FEMS Microbiological Reviews 2007, 31:592-613.
26. Lundström H., Björkroth J. Lactic acid bacteria in marinades used for modified atmosphere packaged broiler chicken meat products. Journal of Food Protection 2007, 70:766-770.
27. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.-J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L.I., Jarvie T.P., Jirage K.B., Kim J.-B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
28. Meyer F., Paarmann D., D'Souza M., Olson R., Glass E.M., Kubal M., Paczian T., Rodriguez A., Stevens R., Wilke A., Wilkening J., Edwards R.A. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9:386.
29. Nieminen T., Vihavainen E., Paloranta A., Lehto J., Paulin L., Auvinen P., Björkroth J. Characterization of bacterial communities in modified-atmosphere packed minced meat with terminal restriction fragment length polymorphism. International Journal of Food Microbiology 2011, 144:360-366.
30. Nychas G.-J.E., Marshall D.L., Sofos J. Meat, poultry, and seafood. Food Microbiology 2007, 105-140. ASM press, Washington, D.C. M. Doyle, L. Beuchat (Eds.).
31. Parks D.H., Beiko R.G. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 2010, 26:715-721.
32. Patsias A., Chouliara I., Badeka A., Savvaidis I.N., Kontominas M.G. Shelf-life of a chilled precooked chicken product stored in air and under modified atmospheres: microbiological, chemical, sensory attributes. Food Microbiology 2006, 23:423-429.
33. Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glöckner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research 2007, 35:7188-7196.
34. Samelis J. Managing microbial spoilage in the meat industry. Food Spoilage Microorganisms 2006, 213-286. Woodhead Publishing, Cambridge. C. Blackburn (Ed.).
35. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Horn D.J.V., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 75:7537-7541.
36. Shendure J., Porreca G.J., Reppas N.B., Lin X., McCutcheon J.P., Rosenbaum A.M., Wang M.D., Zhang K., Mitra R.D., Church G.M. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005, 309:1728-1732.
37. Smith D.B., Acton J.C. Marination, cooking and curing of poultry products. Poultry Meat Processing 2000, 257-280. CRC Press, Boca Raton. A. Sams (Ed.).
38. Smolander M., Alakomi H.-L., Ritvanen T., Vainionpää J., Ahvenainen R. Monitoring of the quality of modified atmosphere packaged broiler chicken cuts stored in different temperature conditions. A. Time-temperature indicators as quality-indicating tools. Food Control 2004, 15:217-229.
39. Sogin M.L., Morrison H.G., Huber J.A., Welch D.M., Huse S.M., Neal P.R., Arrieta J.M., Herndl G.J. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences 2006, 103:12115-12120.
40. Susiluoto T., Korkeala H., Björkroth K.J. Leuconostoc gasicomitatum is the dominating lactic acid bacterium in retail modified-atmosphere-packaged marinated broiler meat strips on sell-by-day. International Journal of Food Microbiology 2003, 80:89-97.
41. Tringe S.G., von Mering C., Kobayashi A., Salamov A.A., Chen K., Chang H.W., Podar M., Short J.M., Mathur E.J., Detter J.C., Bork P., Hugenholtz P., Rubin E.M. Comparative metagenomics of microbial communities. Science 2005, 308:554-557.
42. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., Fouts D.E., Levy S., Knap A.H., Lomas M.W., Nealson K., White O., Peterson J., Hoffman J., Parsons R., Baden-Tillson H., Pfannkoch C., Rogers Y.-H., Smith H.O. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304:66-74.
43. Vihavainen E., Lundström H.-S., Susiluoto T., Koort J., Paulin L., Auvinen P., Björkroth K.J. Role of broiler carcasses and processing plant air in contamination of modified-atmosphere-packaged broiler products with psychrotrophic lactic acid bacteria. Applied and Environmental Microbiology 2007, 73:1136-1145.
44. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology 1991, 173:697-703.