Food Science and Industry (식품과학과 산업)

Korean Society of Food Science and Technology (한국식품과학회)
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Analysis techniques for fermented foods microbiome

발효식품의 마이크로바이옴 분석 기술

  • Cha, In-Tae (Division of Bioengineering, Incheon National University) ;
  • Seo, Myung-ji (Division of Bioengineering, Incheon National University)
  • Received : 2017.02.08
  • Accepted : 2017.03.09
  • Published : 2017.03.31
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Abstract

Human have eaten various traditional fermented foods for a numbers of million years for health benefit as well as survival. The beneficial effects of fermented foods have been resulted from complex microbial communications within the fermented foods. Therefore, the holistic approaches for individual identification and complete microbial profiling involved in their communications have been of interest to food microbiology fields. Microbiome is the ecological community of microorganisms that literally share our environments including foods as well as human body. However, due to the limitation of culture-dependent methods such as simple isolations of just culturable microorganisms, the culture-independent methods have been consistently developed, resulting in new light on the diverse non-culturable and hitherto unknown microorganisms, and even microbial communities in the fermented foods. For the culture-independent approaches, the food microbiome has been deciphered by employing various molecular analysis tools such as fluorescence in situ hybridization, quantitative PCR, and denaturing gradient gel-electrophoresis. More recently, next-generation-sequencing (NGS) platform-based microbiome analysis has been of interest, because NGS is a powerful analytical tool capable of resolving the microbiome in respect to community structures, dynamics, and activities. In this overview, the development status of analysis tools for the fermented food microbiome is covered and research trend for NGS-based food microbiome analysis is also discussed.

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References

  1. Hayes M, Ross RP, Fitzgerald GF, Stanton C. Putting microbes to work: dairy fermentation, cell factories and bioactive peptides. Part I: overview. Biotechnol. J. 2: 426-434 (2007) https://doi.org/10.1002/biot.200600246
  2. Tannock GW. Probiotics and prebiotics: Where are we going?(eds.), Caister Academic Press, Norfork, England (2002)
  3. Hutkins R. Microbiology and Technology of Fermented Foods (Wiley-Blackwell) (2006)
  4. 전체옥. 전통 발표식품의 기능성 향상 및 표준화를 위한 데이터베이스 구축. e-생물산업 27 (2014)
  5. Fleet GH. Microorganisms in food ecosystems. lnt. J. Food Microbiol. 50: 101-117 (1999) https://doi.org/10.1016/S0168-1605(99)00080-X
  6. Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. USA 104: 11436-11440 (2007) https://doi.org/10.1073/pnas.0611525104
  7. Wolfe BE, Dutton RJ. Fermented foods as experimentally tractable microbial ecosystems. Cell 161: 49-55 (2015) https://doi.org/10.1016/j.cell.2015.02.034
  8. De Filippis F, La Storia A, Stellato G, Gatti M, Ercolini D. A selected core microbiome drives the early stages of three popular Italian cheese manufactures. PLoS ONE 9: e89680 (2014) https://doi.org/10.1371/journal.pone.0089680
  9. Jung JY, Lee SH, Kim JM, Park MS, Bae JW, Hahn Y, Madsen EL, Jeon CO. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl. Environ. Microbiol. 77: 2264-2274 (2011) https://doi.org/10.1128/AEM.02157-10
  10. Ciani M, Comitini F, Mannazzu I, Domizio P. Controlled mixed culture fermentation: a new perspective on the use of non-Sac-charomyces yeasts in winemaking. FEMS Yeast Res. 10: 123-133 (2010) https://doi.org/10.1111/j.1567-1364.2009.00579.x
  11. Nemergut DR, Schmidt SK, Fukami T, O'Neill SP, Bilinski TM, Stanish LF, Knelman, JE, Darcy JL, Lynch RC, Wickey P, Ferrenberg S. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77: 342-356 (2013) https://doi.org/10.1128/MMBR.00051-12
  12. Wolfe BE, Button JE, Santarelli M, Dutton RJ. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158: 422-433 (2014) https://doi.org/10.1016/j.cell.2014.05.041
  13. Brehm-Stecher B, Young C, Jaykus LA, Tortorello ML. Sample preparation: the forgotten beginning. J. Food Prot. 11.: 1774-1789(2009)
  14. Wilson IG. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63: 3741-3751 (1997)
  15. Pirondini A, Bonas U, Maestri E, Visioli G, Manniroli M, Marmiroli N. Yield and amplificability of different DNA extraction procedures for traceability in the dairy food chain. Food Control 21: 663-668 (2010) https://doi.org/10.1016/j.foodcont.2009.10.004
  16. Reysenbach AL, Giver LJ, Wickham GS, Pace NR. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58: 3417-3418 (1992)
  17. Scholz MB, Lo CC, Chain PSG. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol. 23: 9-15 (2012) https://doi.org/10.1016/j.copbio.2011.11.013
  18. Zaneveld JR, Parfrey LW, van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R. Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. Trends Microbiol. 19: 472-482 (2011) https://doi.org/10.1016/j.tim.2011.07.006
  19. Nilsson RH, Rybeig M, Kristiaossoo. E, Abareokov K, Larssoo. KH, Koljalg U. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS One 1: e59 (2006) https://doi.org/10.1371/journal.pone.0000059
  20. Bokulich NA, Mills DA. Improved internal transcribed spacer(ITS) primer selection enables quantitative, ultra-high-through-put fungal community profiling. Appl. Environ. Microbiol. 79: 2519-2526 (2013) https://doi.org/10.1128/AEM.03870-12
  21. Rittmann BE, Krajmalnik-Brown R, Halden RU. Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy. Nat. Rev. Microbiol. 6: 604-612 (2008) https://doi.org/10.1038/nrmicro1939
  22. Ercolini D, Hill PJ, Dodd CE. Development of a fluorescence in situ hybridizalion method for cheese using a 16S rRNA probe. J. Microbiol. Methods 52: 267-271 (2003) https://doi.org/10.1016/S0167-7012(02)00162-8
  23. Postollec F, Falentin H, Pavan S, Combrissoo J, Sohier D. Recent advances in quantitative PCR (qPCR) applications in food microbiology. Food Microbiol. 28: 848-861 (2011) https://doi.org/10.1016/j.fm.2011.02.008
  24. Haakensen, MC, Butt L, Chaban B, Deneer H, Ziola B, Dowgiert T. horA-Specific real-time PCR for detection of beer-spoilage latic acid bacteria. J. Am. Soc. Brew. Chem. 65: 157-165 (2007)
  25. Mendes-Ferreira A, Barbosa C, Jimenez-Marti E, Del Olmo ML, Mendes-Faia A. The wine yeast stain-dependent expression of genes implicated in sulfide production in response to nitrogen availability. J. Microbiol. Biotechnol. 20: 1314-1321 (2010) https://doi.org/10.4014/jmb.1003.03039
  26. Muyzer G, Dewaal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel-eletrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S ribosomal RNA. Appl. Environ. Mircrobiol. 59: 695-700 (1993)
  27. Nubel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann Rl, Ludwig W, Backrhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by tem-perature gradient gel electrophoresis. J. Bacteriol. 178: S636-S643 (1996)
  28. Polz MF, Cavanaugh CM. Bias in template-to-product ratios in multi-template PCR. Appl. Environ. Microbiol. 64: 3724-3730 (1998)
  29. Ampe F, Omar NB, Moizan C, Wacher C, Guyot JP. Polyphasic study of the spatial distribution of microorganisms in mexican pozol, a fermented maize dough, demonstrates the need for cultivstion-independent methods to investigate traditional fermentations. Appl. Environ. Microbiol. 65: 5464-5473 (1999)
  30. Cocolin L, Bisson LF, Mills DA. Direct profiling of the yeast dynamics in wine fermentation. FEMS Microbiol. Lett. 189: 81-87 (2000) https://doi.org/10.1111/j.1574-6968.2000.tb09210.x
  31. Renouf V, Claisse O, Miot-Sertier C, Lonvaud-Funel A. Lactic acid bacteria evolution during winemaking: use of rpoB gene as a target for PCR-DGGE analysis. Food Microbiol. 23: 136-145 (2006) https://doi.org/10.1016/j.fm.2005.01.019
  32. Eckburg PB, Bilk EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science 308: 1635-1638 (2005) https://doi.org/10.1126/science.1110591
  33. Roh SW, Kim KH, Nam YD, Chang HW, Park EJ, Bae JW. lnvestigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. ISME J. 4: 1-16 (2010) https://doi.org/10.1038/ismej.2009.83
  34. Niteminen TT, Koskinen K, Laine P, Hultman J, Sade E, Paulin L, Paloranta A, Johansson P, Bjorkroth J, Auvinen P. Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics. Int. J. Food Microbiol. 157: 142-149 (2012) https://doi.org/10.1016/j.ijfoodmicro.2012.04.016
  35. Danilo E. High-throughput sequencing and metagenomics moving forward in the culture-independent analysis of food microbial ecology. Appl. Environ. Microbiol. 79: 3148-3155 (2013) https://doi.org/10.1128/AEM.00256-13