Metagenomic analysis of kimchi, a Traditional Korean fermented food

Applied and Environmental Microbiology

Volumn 77, Issue 7, 2011, Pages 2264-2274

  Jung, Ji Young ^a   Lee, Se Hee ^a   Kim, Jeong Myeong ^a   Park, Moon Su ^a   Bae, Jin Woo ^b   Hahn, Yoonsoo ^a   Madsen, Eugene L ^c   Jeon, Che Ok ^a  

^a Chung Ang University   (South Korea)

^b Kyung Hee University   (South Korea)

^c Cornell University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; BACTERIAL POPULATION; FERMENTATION PROCESS; FERMENTATION PRODUCTS; FERMENTED FOODS; LACTIC ACID FERMENTATION; LACTOBACILLUS SAKEI; LEUCONOSTOC; LEUCONOSTOC MESENTEROIDES; METAGENOMES; METAGENOMIC ANALYSIS; METAGENOMIC DNA; MICROBIAL COMMUNITIES; MICROBIAL GENOMES; PHYLOGENETIC ANALYSIS; SUBSYSTEM TECHNOLOGY; TRADITIONAL FOOD;

BACTERIOPHAGES; CARBOHYDRATES; CELL CULTURE; DNA SEQUENCES; ETHANOL; EXTRACTION; GENES; LACTIC ACID; NUCLEIC ACIDS; PROCESS CONTROL; RNA; TITANIUM;

FERMENTATION;

BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

BACTERIOPHAGE; BACTERIUM; ETHANOL; FERMENTATION; FOOD SAFETY; GENOME; MICROBIAL COMMUNITY; PHYLOGENETICS;

ARTICLE; BACTERIOPHAGE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; FOOD CONTROL; GENETICS; KOREA; METAGENOME; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

BACTERIA; BACTERIOPHAGES; BIODIVERSITY; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FOOD MICROBIOLOGY; KOREA; METAGENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); LACTOBACILLUS; LACTOBACILLUS SAKEI SUBSP. SAKEI 23K; LEUCONOSTOC; LEUCONOSTOC MESENTEROIDES; LEUCONOSTOC MESENTEROIDES SUBSP. MESENTEROIDES ATCC 8293; WEISSELLA;

EID: 79953291919     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02157-10     Document Type: Article

References (61)

1. Aziz, R. K., et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75.
2. Bae, J. W., et al. 2005. Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl. Environ. Microbiol. 71:8825-8835.
3. Bamford, D. H., J. M. Grimes, and D. I. Stuart. 2005. What does structure tell us about virus evolution? Curr. Opin. Struct. Biol. 15:655-663.
4. Chaillou, S., et al. 2005. The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K. Nat. Biotechnol. 23:1527-1533.
5. Cho, J., et al. 2006. Microbial population dynamics of kimchi, a fermented cabbage product. FEMS Microbiol. Lett. 257:262-267.
6. Chou, H. H., and M. H. Holmes. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17:1093-1104.
7. Cole, J. R., et al. 2009. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145.
8. Costello, E. K., et al. 2009. Bacterial community variation in human body habitats across space and time. Science 326:1694-1697.
9. DeLong, E. F., et al. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311:496-503.
10. Dinsdale, E. A., et al. 2008. Functional metagenomic profiling of nine biomes. Nature 452:629-632.
11. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
12. Ercolini, D. 2004. PCR-DGGE fingerprinting: novel strategies for detection of microbes in food. J. Microbiol. Methods 56:297-314.
13. Farrelly, V., F. A. Rainley, and E. Stackebrandt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:2798-2801.
14. 1H NMR, a rapid method to monitor organic acids during cupuassu (Theobroma grandiflorum Spreng) processing. J. Agric. Food. Chem. 54:4102-4106.
15. García Martín, H., et al. 2006. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol. 24:1263-1269.
16. Ghai, R., et al. 2010. Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME J. 4:1154-1166.
17. Gomez-Alvarez, V., T. K. Teal, and T. M. Schmidt. 2009. Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3:1314-1317.
18. Grissa, I., G. Vergnaud, and C. Pourcel. 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35:W52-W57.
19. Ha, J. H., W. S. Hawer, Y. J. Kim, and Y. J. Nam. 1989. Changes of free sugars in kimchi during fermentation. Korean J. Food Sci. Technol. 21:633-638.
20. Juck, D., T. Charles, L. G. Whyte, and C. W. Greer. 2000. Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities. FEMS Microbiol. Ecol. 33:241-249.
21. Kim, J., J. Chun, and H. U. Han. 2000. Leuconostoc kimchii sp. nov., a new species from kimchi. Int. J. Syst. Evol. Microbiol. 50:1915-1919.
22. Kim, J. F., et al. 2008. Complete genome sequence of Leuconostoc citreum KM20. J. Bacteriol. 190:3093-3094.
23. Kim, M., and J. Chun. 2005. Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis. Int. J. Food Microbiol. 103:91-96.
24. Kim, N., K. R. Park, I. S. Park, Y. J. Cho, and Y. M. Bae. 2005. Application of a taste evaluation system to the monitoring of Kimchi fermentation. Biosens. Bioelectron. 20:2283-2291.
25. Lee, J.-S., et al. 1997. Classification of isolates originating from kimchi using carbon-source utilization patterns. J. Microbiol. Biotechnol. 7:68-74.
26. Lee, J., et al. 2002. Weissella koreensis sp. nov., isolated from kimchi. Int. J. Syst. Evol. Microbiol. 52:1257-1261.
27. Lee, J. S., et al. 2005. Analysis of kimchi microflora using denaturing gradient gel electrophoresis. Int. J. Food Microbiol. 102:143-150.
28. Lee, D., S. Kim, J. Cho, and J. Kim. 2008. Microbial population dynamics and temperature changes during fermentation of kimjang kimchi. J. Microbiol. 46:590-593.
29. 1H NMR metabolite fingerprinting and profiling analysis. J. Agric. Food Chem. 57:7513-7522.
30. Li, W. Z., and A. Godzik. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659.
31. Lu, Z., F. Breidt, V. Plengvidhya, and H. P. Flaming. 2003. Bacteriophage ecology in commercial sauerkraut fermentations. Appl. Environ. Microbiol. 69:3192-3202.
32. Lu, Z., E. Altermann, F. Breidt, and S. Kozyavkin. 2010. Sequence analysis of Leuconostoc mesenteroides bacteriophage σ1-A4 isolated from an industrial vegetable fermentation. Appl. Environ. Microbiol. 76:1955-1966.
33. Makarova, K., et al. 2006. Comparative genomics of the lactic acid bacteria. Proc. Natl. Acad. Sci. U. S. A. 103:15611-15616.
34. McFeeters, R. F., and K.-H. Chen. 1986. Utilization of electron acceptors for anaerobic mannitol metabolism by Lactobacillus plantarum: compounds which serve as electron acceptors. Food Sci. 3:73-81.
35. Meyer, F., et al. 2008. The metagenomics RAST server: a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386-394.
36. Mou, X., S. L. Sun, R. A. Edwards, R. E. Hodson, and M. A. Moran. 2008. Bacterial carbon processing by generalist species in the coastal ocean. Nature 451:708-711.
37. Mudgal, P., F. Jr., Breidt, S. R. Lubkin, and K. P. Sandeep. 2006. Quantifying the significance of phage attack on starter cultures: a mechanistic model for population dynamics of phage and their hosts isolated from fermenting sauerkraut. Appl. Environ. Microbiol. 72:3908-3915.
38. Nam, Y. D., H. W. Chang, K. H. Kim, S. W. Roh, and J. W. Bae. 2009. Metatranscriptome analysis of lactic acid bacteria during kimchi fermentation with genome-probing microarrays. Int. J. Food Microbiol. 130:140-146.
39. Niu, B., L. Fu, S. Sun, and W. Li. 2010. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 11:187-198.
40. Park, K. Y., et al. 2003. Kimchi and an active component, beta-sitosterol, reduce oncogenic H-Ras(v12)-induced DNA synthesis. J. Med. Food. 6:151-156.
41. Park, E. J., et al. 2009. Application of quantitative real-time PCR for enumeration of total bacterial, archaeal, and yeast populations in kimchi. J. Microbiol. 47:682-685.
42. Park, J. M., et al. 2010. Identification of the lactic acid bacteria in kimchi according to initial and over-ripened fermentation using PCR and 16S rRNA gene sequence analysis. Food Sci. Biotechnol. 19:541-546.
43. Parsley, L. C., et al. 2010. Census of the viral metagenome within an activated sludge microbial assemblage. Appl. Environ. Microbiol. 76: 2673-2677.
44. Parsley, L. C., et al. 2010. Identification of diverse antimicrobial resistance determinants carried on bacterial, plasmid, or viral metagenomes from an activated sludge microbial assemblage. Appl. Environ. Microbiol. 76:3753-3757.
45. Qin, J., et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65.
46. Ritalahti, K. M., et al. 2006. Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Appl. Environ. Microbiol. 72:2765-2774.
47. Rodriguez-Brito, B., et al. 2010. Viral and microbial community dynamics in four aquatic environments. ISME J. 4:739-751.
48. Roh, S. W., et al. 2010. Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. ISME J. 4:1-16.
49. Sanapareddy, N., et al. 2009. Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. Appl. Environ. Microbiol. 75:1688-1696.
50. Shendure, J., and H. Ji. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145.
51. Shin, M. S., S. K. Han, J. S. Ryu, K. S. Kim, and W. K. Lee. 2008. Isolation and partial characterization of a bacteriocin produced by Pediococcus pentosaceus K23-2 isolated from kimchi. J. Appl. Microbiol. 105:331-339.
52. Simon, C., A. Wiezer, A. W. Strittmatter, and R. Daniel. 2009. Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Appl. Environ. Microbiol. 75:7519-7526.
53. 1H nuclear magnetic resonance-based metabolomic characterization of wines by grape varieties and production areas. J. Agric. Food Chem. 56:8007-8016.
54. Song, Y.-O. 2004. The functional properties of kimchi for the health benefits. J. Food Sci. Nutr. 9:27-33.
55. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
56. Tringe, S. G., et al. 2005. Comparative metagenomics of microbial communities. Science 308:554-557.
57. Tyson, G. W., et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43.
58. Tyson, G. W., and J. F. Banfield. 2008. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ. Microbiol. 10:200-207.
59. Venter, J. C., et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
60. Wilmes, P., S. L. Simmons, V. J. Denef, and J. F. Banfield. 2009. The dynamic genetic repertoire of microbial communities. FEMS Microbiol. Rev. 33:109-132.
61. Wisselink, H. W., R. A. Weusthuis, G. Eggink, J. Hugenholtz, and G. J. Grobben. 2002. Mannitol production by lactic acid bacteria: a review. Int. Dairy J. 12:151-161.