Journal of Dairy Science and Biotechnology

Korean Society of Dairy Science and Biotechnology (한국낙농식품응용생물학회)
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Perspective on Rapid and Selective Method for Detecting Microbiology in Dairy Industry: A Review

낙농산업에 필요한 미생물 검사방법과 전망: 총설

  • Chon, Jung-Whan (KU Center for Food Safety and College of Veterinary Medicine, Konkuk University) ;
  • Kim, Hyun-Sook (Dept. of Veterinary Physiology, College of Veterinary Medicine, Konkuk University) ;
  • Kim, Hong-Seok (KU Center for Food Safety and College of Veterinary Medicine, Konkuk University) ;
  • Kim, Dong-Hyeon (KU Center for Food Safety and College of Veterinary Medicine, Konkuk University) ;
  • Song, Kwang-Young (KU Center for Food Safety and College of Veterinary Medicine, Konkuk University) ;
  • Yim, Jin-Hyuk (KU Center for Food Safety and College of Veterinary Medicine, Konkuk University) ;
  • Choi, Dasom (KU Center for Food Safety and College of Veterinary Medicine, Konkuk University) ;
  • Lim, Jong-Soo (KU Center for Food Safety and College of Veterinary Medicine, Konkuk University) ;
  • Jeong, Dong-Gwan (Dept. of Food & Nutrition, College of Natural Science, Kosin University) ;
  • Kim, Soo-Ki (Dept. of Animal Science & Technology, College of Animal Bioscience & Technology, Konkuk University) ;
  • Seo, Kun-Ho (KU Center for Food Safety and College of Veterinary Medicine, Konkuk University)
  • 천정환 (건국대학교 수의과대학 및 KU 식품안전연구소) ;
  • 김현숙 (건국대학교 수의과대학 수의생리학전공) ;
  • 김홍석 (건국대학교 수의과대학 및 KU 식품안전연구소) ;
  • 김동현 (건국대학교 수의과대학 및 KU 식품안전연구소) ;
  • 송광영 (건국대학교 수의과대학 및 KU 식품안전연구소) ;
  • 임진혁 (건국대학교 수의과대학 및 KU 식품안전연구소) ;
  • 최다솜 (건국대학교 수의과대학 및 KU 식품안전연구소) ;
  • 임종수 (건국대학교 수의과대학 및 KU 식품안전연구소) ;
  • 정동관 (고신대학교 자연과학대학 식품영양학과) ;
  • 김수기 (건국대학교 동물생명과학대학 동물자원학과) ;
  • 서건호 (건국대학교 수의과대학 및 KU 식품안전연구소)
  • Received : 2015.05.30
  • Accepted : 2015.06.15
  • Published : 2015.06.30
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Abstract

To date, detection of microbial populations in dairy products has been performed using culture media, which is a time-consuming and laborious method. The recently developed chromogenic media could be more rapid and specific than classical culture media. However, the newly developed molecular-based technology can detect microbial populations with greater rapidity and sensitivity than the classical method involving culture media and chromogenic media. This molecular-based technology could provide various options for monitoring the characterization of different states of bacteria and cells. Thus, it could help upgrade the processing system of the dairy industry so as to maintain the safety and quality of dairy foods. Among the various newly developed molecular-based technologies, flow cytometry can potentially be used for monitoring microbiological populations in the dairy industry if official international standards are available for this purpose. When omics technology would have biomarker identification, it could be regarded as the rapid and sensitive analytical methods. Methods based on PCR, which has become a basic technique in microbiological research, can be developed and validated as alternative methods for quantification of dairy microorganisms. This review discusses methods for monitoring microbiological populations in dairy foods and the limitations of these studies, as well as the need for further research on such methods in the dairy industry.

낙농 미생물학에서 사용하는 주요 분석 방법들에 대한 지속적인 개정이 요구되어지고 있는 것이 사실이다. 현재 이용 가능한 자료들을 바탕으로 균주의 생리 및 대사 특성을 더 깊이 이해할 수 있으며, LAB와 probiotic 생리적 상태를 측정할 수 있는 기술을 개발할 수 있다. 예를 들어, 고유 균주의 생화학 반응으로부터 얻은 생물학적 생리학적 지식을 바탕으로 발색형광배지(chromogenic media)의 개발이 가능하다. 이 기술은 오랫동안 사용되어온 한천 배지보다 사용법이 간단하며, 미생물을 제어할 수 있다. 유망한 유동세포계수법(flow cytometry, FC) 기술은 우유, 요구르트, 그 외 발효 유제품의 혼합 배양의 분석에 뛰어나다. 이 기술은 공정 과정 중에 또는 생산품의 유통 기한 관리에 사용될 수 있지만, 이 기술을 사용하기 위해서는 우유 단백질에 의해서 생성되는 인공 산물을 방지하기 위해 최적화 되어야 한다. 또한 유동세포계수법(flow cytometry, FC)은 정량 한계가 높기 때문에, 현재 사용하고 있는 탐침(probe)은 종 또는 속이 아닌 표적 세포 구성을 분석한다. 따라서 유동세포계수법(flow cytometry, FC)은 특정 물질의 계수보다는 생리적 상태를 측정에 더 적합한 기술이라고 볼 수 있다. Omics 자료를 통해 생리적 상태를 더 신속하게 측정할 수 있는 핵심적인 생체지표 확인이 가능해졌다. PCR은 이미 식품매개 병원균 및 부패균의 검출에 일상적으로 사용되고 있다. 이 기술은 더욱 나아가 발효균 및 probiotic 박테리아 검출에도 사용되어 핵산 추출, PCR 과정, 자료 해석을 표준화 시킬 수 있으며, 또한 다른 기술에 비해 PCR은 표적 발효 균주를 더 신속하게 선택하며, 공정 과정을 최적상태로 유지시킬 수 있을 것이다. LAB와 probiotic의 적응성 및 생리적 상태의 연구에 필요한 기준, 특허품, 상업화된 신속분석장치(kit)는 아직까지 개발되지 않았다. 본 총설 논문에서는 여러 가지 기술을 검토함으로써 이 모든 기술에는 2가지 주요한 요인이 있다. 첫 번째는 낙농업 산업의 특정 요구에 따른 방법의 평가이며, 두 번째는 공식적인 기준에 따른 검증이다. 사실상 식품매개 병원균의 특성 분석에 사용될 수 있는 표준법이 개발되고 검증되었지만, LAB, probiotic 등의 박테리아 분석에 있어서 표준화된 방법과 진단산업과의 연관성이 부족한 것이 사실이다. 낙농 업계에 의해서 수행되어진 품질관리의 양을 고려해 볼 때 이것은 매우 중요하게 인식되어야 할 부분이다.

Keywords

References

  1. Antunes, A. E. C., Grael, E. T., Moreno, I., Rodrigues, L. G., Dourado, F. M. and Saccaro, D. M. 2007. Selective enumeration and viability of Bifidobacterium animalis subsp. lactis in a new fermented milk product. Braz. J. Microbiol. 38:173-177. https://doi.org/10.1590/S1517-83822007000100035
  2. Ashraf, R. and Shah, N. P. 2011. Selective and differential enumerations of Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus casei and Bifidobacterium spp. in yoghurt -a review. Int. J. Food Microbiol. 149:194-208. https://doi.org/10.1016/j.ijfoodmicro.2011.07.008
  3. Atkinson, A., Colburn, W. A., Degruttola, V. G., Demets, D. L., Downing, G. J. and Hoth, D. F. 2001. Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin. Pharmacol. Ther. 69:89-95. https://doi.org/10.1067/mcp.2001.113989
  4. Baker, M. 2012. Digital PCR hits its stride. Nat. Methods 9:541-544. https://doi.org/10.1038/nmeth.2027
  5. Bartlett, J. M., and Stirling, D. 2003. A short history of the polymerase chain reaction. Methods Mol. Biol. 226:3-6.
  6. Bernardeau, M., Vernoux, J. P., and Gueguen, M. 2001. Usefulness of epifluorescence for quantitative analysis of lactobacilli in probiotic feed. J. Appl. Microbiol. 91:1103-1109. https://doi.org/10.1046/j.1365-2672.2001.01481.x
  7. Bove, C. G., Lazzi, C., Bernini, V., Bottari, B., Neviani, E. and Gatti, M. 2011. cDNA-amplified fragment length polymorphism to study the transcriptional responses of Lactobacillus rhamnosus growing in cheese-like medium. J. Appl. Microbiol. 111:855-864. https://doi.org/10.1111/j.1365-2672.2011.05101.x
  8. Boyer, M. and Combrisson, J. 2013. Analytical opportunities of quantitative polymerase chain reaction in dairy microbiology. Int. Dairy J. 30:45-52. https://doi.org/10.1016/j.idairyj.2012.11.008
  9. Caplice, E. and Fitzgerald, G. F. 1999. Food fermentations: role of microorganisms in food production and preservation. Int. J. Food Microbiol. 15:131-149.
  10. Champagne, C. P., Ross, R. P., Saarela, M., Hansen, K. F. and Charalampopoulos, D. 2011. Recommendations for the viability assessment of probiotics as concentrated cultures and in food matrices. Int. J. Food Microbiol. 149:185-193. https://doi.org/10.1016/j.ijfoodmicro.2011.07.005
  11. Chon, J. W., Song, K. Y., Kim, S. Y., Hyeon, J. Y. and Seo, K. H. 2012. Isolation and characterization of Cronobacter from desiccated foods in Korea. J. Food Sci. 77:M354-358. https://doi.org/10.1111/j.1750-3841.2012.02750.x
  12. Davey, H. M. 2011. Life, death, and in-between: meanings and methods in microbiology. Appl. Environ. Microbiol. 77:5571-5576. https://doi.org/10.1128/AEM.00744-11
  13. de Vos, W. M. 2011. Systems solutions by lactic acid bacteria: from paradigms to practice. Microb. Cell Fact. 10(Suppl. 1): S2. https://doi.org/10.1186/1475-2859-10-S1-S2
  14. Diaz, M., Herrero, M., Garcia, L. A. and Quiros, C. 2010. Application of flow cytometry to industrial microbial bioprocesses. Biochem. Eng. J. 48:385-407. https://doi.org/10.1016/j.bej.2009.07.013
  15. do Espirito Santo, A. P., Perego, P., Converti, A. and Oliveira, M. N. 2011. Influence of food matrices on probiotic viability - a review focusing on the fruity bases. Trends Food Sci. Technol. 22:377-385. https://doi.org/10.1016/j.tifs.2011.04.008
  16. Doherty, S. B., Wang, L., Ross, R. P., Stanton, C., Fitzgerald, G. F. and Brodkorb, A. 2010. Use of viability staining in combination with flow cytometry for rapid viability assessment of Lactobacillus rhamnosus GG in complex protein matrices. J. Microbiol. Methods 82:301-310. https://doi.org/10.1016/j.mimet.2010.07.003
  17. El Arbi, A., Ghorbal, S., Delacroix-Buchet, A. and Bouix, M. 2011. Assessment of the dynamics of the physiological states of Lactococcus lactis ssp. cremoris SK11 during growth by flow cytometry. J. Appl. Microbiol. 111:1205-1211. https://doi.org/10.1111/j.1365-2672.2011.05114.x
  18. Fittipaldi, M., Nocker, A. and Codony, F. 2012. Progress in understanding preferential detection of live cells using viability dyes in combination with DNA amplification. J. Microbiol. Methods 91:276-289. https://doi.org/10.1016/j.mimet.2012.08.007
  19. Forssten, S. D., Sindelar, C. W. and Ouwehand, A. C. 2011. Probiotics from an industrial perspective. Anaerobe 17:410-413. https://doi.org/10.1016/j.anaerobe.2011.04.014
  20. Garcia-Hernandez, J., Moreno, Y., Amorocho, C. M. and Hernandez, M. 2012. A combination of direct viable count and fluorescence in situ hybridization for specific enumeration of viable Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. Lett. Appl. Microbiol. 54:247-254. https://doi.org/10.1111/j.1472-765X.2011.03201.x
  21. Glenn, M., Havukkala, I. J., Lubbers, M. W. and Dekker, J. 2004. Polynucleotides and polypeptides derived from Lactobacillus rhamnosus HN001. WO2004031389. NZ patent application.
  22. Hayden, R. T., Gu, Z., Ingersoll, J., Abdul-Ali, D., Shi, L. and Pounds, S. 2013. Comparison of droplet digital PCR to real-time PCR for quantitative detection of cytomegalovirus. J. Clin. Microbiol. 51:540-546. https://doi.org/10.1128/JCM.02620-12
  23. Huggett, J. F., Foy, C. A., Benes, V., Emslie, K., Garson, J. A. and Haynes, R. 2013. The digital MIQE guidelines: minimum information for publication of quantitative digital PCR experiments. Clin. Chem. 59:892-902. https://doi.org/10.1373/clinchem.2013.206375
  24. International Dairy Federation (IDF). 2012. IDF Programme of Work (available at: http://www.ukidf.org/documents/pow_ Sep12.pdf).
  25. ISO. 2007. Microbiology of Food and Animal Feeding Stuffs - General Requirements and Guidance for Microbiological Examinations. Geneva: International Standardisation Organisation.
  26. ISO. 2011. Microbiology of Food and Animal Feeding Stuffs - Real-Time Polymerase Chain Reaction (PCR) for the Detection of Food-Borne Pathogens -General Requirements and Definitions. Geneva: International Standardisation Organisation.
  27. ISO. 2013. Microbiology of Food and Animal Feed - Horizontal Method for Determination of Hepatitis AVirus and Norovirus in Food using Real-Time RT-PCR - Part 1: Method for Quantification. Geneva: International Standardisation Organisation.
  28. Karimi, R., Mortazavian, A. M. and Amiri-Rigi, A. 2012. Selective enumeration of probiotic microorganisms in cheese. Food Microbiol. 29:1-9.
  29. Kim, Y. J., Chon, J. W., Lim, J. S., Song, B. R., Seo, K. H., Heo, E. J., Park, H. J., Wee, S. H., Oh, D. H. and Moon, J. S. 2015. Traceback investigation for Salmonella contamination at egg processing plants in South Korea: prevalence, antibiotic resistance, and epidemiological tracing by rep-PCR fingerprinting. J. Food Sci. 80:M759-764. https://doi.org/10.1111/1750-3841.12731
  30. Klaenhammer, T. R., Altermann, E., Azcarate-Peril, A., McAuliffe, O. and Russell, W. M. 2005. Lactobacillus acidophilus nucleic acid sequences encoding stress-related proteins and uses therefore. WO2005086794. USA patent application.
  31. Klaenhammer, T. R., Russell, W. M., Altermann, E. and Azcarate-Peril, A. 2010. Nucleic acids encoding two-component sensing and regulatory proteins, antimicrobial proteins and uses therefore. US 20100279349 A1.
  32. Kramer, M., Obermajer, N., Bogovic Matijasic, B., Rogelj, I. and Kmetec, V. 2009. Quantification of live and dead probiotic bacteria in lyophilised product by realtime PCR and by flow cytometry. Appl. Microbiol. Biotechnol. 84: 1137-1147. https://doi.org/10.1007/s00253-009-2068-7
  33. Lahtinen, S. J., Ouwehand, A. C., Reinikainen, J. P., Korpela, J. M., Sandholm, J. and Salminen, S. J. 2006. Intrinsic properties of so-called dormant probiotic bacteria, determined by flow cytometric viability assays. Appl. Environ. Microbiol. 72:5132-5134. https://doi.org/10.1128/AEM.02897-05
  34. Le Drean, G., Mounier, J., Vasseur, V., Arzur, D., Habrylo, O. and Barbier, G. 2010. Quantification of Penicillium camemberti and P. roqueforti mycelium by realtime PCR to assess their growth dynamics during ripening cheese. Int. J. Food Microbiol. 138:100-107. https://doi.org/10.1016/j.ijfoodmicro.2009.12.013
  35. Lee, K., Rho, B. S., Pi, K., Kim, H. J. and Choi, Y. J. 2011. Proteomic analysis of protein expression in Lactobacillus plantarum in response to alkaline stress. J. Biotechnol. 153: 1-7. https://doi.org/10.1016/j.jbiotec.2011.02.008
  36. Li, J. S., Bi, Y. T., Dong, C., Yang, J. F. and Liang, W. D. 2011. Transcriptome analysis of adaptive heat shock response of Streptococcus thermophilus. PLoS ONE 6:e25777. https://doi.org/10.1371/journal.pone.0025777
  37. Maecker, H. T., Frey, T., Nomura, L. E. and Trotter, J. 2004. Selecting fluorochrome conjugates for maximum sensitivity. Cytometry A 62:169-173.
  38. Masoud, W., Takamiya, M., Vogensen, F. K., Lillevang, S., Al-Soud, W. A. and Sorensen, S. J. 2011. Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing. Int. Dairy J. 21:142-148. https://doi.org/10.1016/j.idairyj.2010.10.007
  39. Maukonen, J., Alakomi, H. -L., Nohynek, L., Hallamaa, K., Leppamaki, S. and Matto, J. 2006. Suitability of the fluorescent techniques for the enumeration of probiotic bacteria in commercial non-dairy drinks and in pharmaceutical products. Food Res. Int. 39:22-32. https://doi.org/10.1016/j.foodres.2005.05.006
  40. Meng, X., Pang, R., Wang, C. and Wang, L. 2010. Rapid and direct quantitative detection of viable bifidobacteria in probiotic yogurt by combination of ethidium monoazide and real-time PCR using a molecular beacon approach. J. Dairy Res. 77:498-504. https://doi.org/10.1017/S0022029910000658
  41. Oberg, C. J., Moyes, L. V., Domek, M. J., Brothersen, C. and McMahon, D. J. 2011. Survival of probiotic adjunct cultures in cheese and challenges in their enumeration using selective media. J. Dairy Sci. 94:2220-2230. https://doi.org/10.3168/jds.2010-3934
  42. Postgate, J. R., Crumpton, J. E. and Hunter, J. R. 1961. The measurement of bacterial viabilities by slide culture. J. Gen. Microbiol. 24:15-24. https://doi.org/10.1099/00221287-24-1-15
  43. Postollec, F., Falentin, H., Pavan, S., Combrisson, J. and Sohier, D. 2011. Recent advances in quantitative PCR (qPCR) applications in food microbiology. Food Microbiol. 28:848-861. https://doi.org/10.1016/j.fm.2011.02.008
  44. Reimann, S., Grattepanche, F., Rezzonico, E. and Lacroix, C. 2010. Development of a real-time RT-PCR method for enumeration of viable Bifidobacterium longum cells in different morphologies. Food Microbiol. 27:236-242. https://doi.org/10.1016/j.fm.2009.10.010
  45. Ruiz, L., Sanchez, B., De Los Reyes-Gavilan, C. G., Gueimonde, M. and Margolles, A. 2009. Coculture of Bifidobacterium longum and Bifidobacterium breve alters their protein expression profiles and enzymatic activities. Int. J. Food Microbiol. 133:148-153. https://doi.org/10.1016/j.ijfoodmicro.2009.05.014
  46. Saccaro, D. M., Hirota, C. Y., Tamime, A. Y. and De Oliveira, M. N. 2011. Evaluation of different selective media for enumeration of probiotic micro-organisms in combination with yogurt starter cultures in fermented milk. African J. Microbiol. Res. 6:2239-2245.
  47. Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L. and Garrett, W. S. 2011. Metagenomic biomarker discovery and explanation. Genome Biol. 12:R60. https://doi.org/10.1186/gb-2011-12-6-r60
  48. Smith, C. J. and Osborn, A. M. 2009. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiol. Ecol. 67:6-20. https://doi.org/10.1111/j.1574-6941.2008.00629.x
  49. Sohier, D., Jamet, E., Le Dizes, A-S., Dizin, M., Pavan, S. and Postollec, F. 2012. Polyphasic approach for quantitative analysis of obligately heterofermentative Lactobacillus species in cheese. Food Microbiol. 31:271-277. https://doi.org/10.1016/j.fm.2012.01.009
  50. Sohier, D., Pavan, S., Riou, A., Combrisson, J. and Postollec, F. 2014 Evolution of microbiological analytical methods for dairy industry needs. Front. Microbiol. 5:16.
  51. Song, K. Y., Hyeon, J. Y., Shin, H. C., Park, C. K., Choi, I. S. and Seo, K. H. 2008. Evaluation of a chromogenic medium supplemented with glucose for detecting Enterobacter sakazakii. J. Microbiol. Biotechnol. 18:579-584.
  52. Song, L., Shan, D., Zhao, M., Pink, B. A., Minnehan, K. A. and York, L. 2013. Direct detection of bacterial genomic DNA at sub-femtomolar concentrations using single molecule arrays. Anal. Chem. 85:1932-1939. https://doi.org/10.1021/ac303426b
  53. Sunny-Roberts, E. O. and Knorr, D. 2008. Evaluation of the response of Lactobacillus rhamnosus VTT E-97800 to sucrose-induced osmotic stress. Food Microbiol. 25:183-189. https://doi.org/10.1016/j.fm.2007.05.003
  54. Taibi, A., Dabour, N., Lamoureux, M., Roy, D. and Lapointe, G. 2011. Comparative transcriptome analysis of Lactococcus lactis subsp. cremoris strains under conditions simulating Cheddar cheese manufacture. Int. J. Food Microbiol. 146: 263-275. https://doi.org/10.1016/j.ijfoodmicro.2011.02.034
  55. Thevenard, B., Rasoava, N., Fourcassie, P., Monnet, V., Boyaval, P. and Rul, F. 2011. Characterization of Streptococcus thermophilus two-component systems in silico analysis, functional analysis and expression of response regulator genes in pure or mixed culture with its yogurt partner, Lactobacillus delbrueckii subsp. bulgaricus. Int. J. Food Microbiol. 151: 171-181. https://doi.org/10.1016/j.ijfoodmicro.2011.08.019
  56. Thierry, A., Deutsch, S. M., Falentin, H., Dalmasso, M., Cousin, F. J. and Jan, G. 2011. New insights into physiology and metabolism of Propionibacterium freudenreichii. Int. J. Food Microbiol. 149:19-27. https://doi.org/10.1016/j.ijfoodmicro.2011.04.026
  57. Tracy, B. P., Gaida, S. M. and Papoutsakis, E. T. 2010. Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. Curr. Opin. Biotechnol. 21:85-99. https://doi.org/10.1016/j.copbio.2010.02.006
  58. Van de Casteele, S., Vanheuverzwijn, T., Ruyssen, T., Van Assche, P., Swings, J. and Huys, G. 2006. Evaluation of culture media for selective enumeration of probiotic strains of lactobacilli and bifidobacteria in combination with yoghurt or cheese starters. Int. Dairy J. 16:1470-1476. https://doi.org/10.1016/j.idairyj.2005.12.002
  59. White, R. A. III, Blainey, P. C., Fan, H. C. and Quake, S. R. 2009. Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics 10:116. https://doi.org/10.1186/1471-2164-10-116
  60. Wong, M. L. and Medrano, J. F. 2005. Real-time PCR for mRNA quantitation. Biotechniques 39:75-85. https://doi.org/10.2144/05391RV01
  61. Zhong, Q., Bhattacharya, S., Kotsopoulos, S., Olson, J., Taly, V. and Griffiths, A. D. 2011. Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR. Lab Chip 11:2167-2174. https://doi.org/10.1039/c1lc20126c
  62. Zotta, T., Guidone, A., Tremonte, P., Parente, E. and Ricciardi, A. 2012. A comparison of fluorescent stains for the assessment of viability and metabolic activity of lactic acid bacteria. World J. Microbiol. Biotechnol. 28:919-927. https://doi.org/10.1007/s11274-011-0889-x