Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Identification of LAB and Fungi in Laru, a Fermentation Starter, by PCR-DGGE, SDS-PAGE, and MALDI-TOF MS

  • Ahmadsah, Lenny S.F. (Department of Food Science and Biotechnology & Institute of Life Sciences and Resources, Kyung Hee University) ;
  • Kim, Eiseul (Department of Food Science and Biotechnology & Institute of Life Sciences and Resources, Kyung Hee University) ;
  • Jung, Youn-Sik (Department of Food Science and Biotechnology & Institute of Life Sciences and Resources, Kyung Hee University) ;
  • Kim, Hae-Yeong (Department of Food Science and Biotechnology & Institute of Life Sciences and Resources, Kyung Hee University)
  • Received : 2017.05.16
  • Accepted : 2017.10.27
  • Published : 2018.01.28
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Abstract

Samples of Laru (a fermentation starter) obtained from the upper part of Borneo Island were analyzed for their lactic acid bacteria (LAB) and fungal diversity using both a culture-independent method (PCR-DGGE) and culture-dependent methods (SDS-PAGE and MALDI-TOF MS). Pediococcus pentosaceus, Lactobacillus brevis, Saccharomycopsis fibuligera, Hyphopichia burtonii, and Kodamaea ohmeri were detected by all three methods. In addition, Weissella cibaria, Weissella paramesenteroides, Leuconostoc citreum, Leuconostoc mesenteroides, Lactococcus lactis, Rhizopus oryzae/Amylomyces rouxii, Mucor indicus, and Candida intermedia were detected by PCR-DGGE. In contrast, Lactobacillus fermentum, Lactobacillus plantarum, Pichia anomala, Candida parapsilosis, and Candida orthopsilosis were detected only by the culture-dependent methods. Our results indicate that the culture-independent method can be used to determine whether multiple laru samples originated from the same manufacturing region; however, using the culture-independent and the two culture-dependent approaches in combination provides a more comprehensive overview of the laru microbiota.

Keywords

References

  1. Abu Bakar HJH. 1989. Studies on the microflora and chemical changes in the fermentation of steamed rice, using laru and lookpaeng as the starter cultures. University of Surrey, United Kingdom.
  2. Merican Z, Yeoh QL. 1989. Tapai processing in Malaysia: a technology in transition. In Steinkraus KH (ed.). Industrialization of Indigenous Fermented Food. Marcel Dekker, New York, NY.
  3. Ko KD. 1972. Tape fermentation. Appl. Microbiol. 23: 976-978.
  4. Saono S, Hull RR, Dhamcaree B. 1986. A Concise Handbook of Indigenous Fermented Food in the Asia Countries. Indonesian Institute of Sciences, Jakarta, Indonesia.
  5. Hesseltine CW, Wang HL. 1986. Indigenous Fermented Foods of Non-Western Origin. Mycologia Memoir No. 11 J. Cramer, Berlin and Stuttgart.
  6. Lotong N. 1992. Seed Inoculum and Their Production Technology [in Thai], 2nd Ed. Funny Publishing, Bangkok, Thailand.
  7. Saono G, Gandjar I, Basuki T, Karsono H. 1974. Mycoflora of ragi and some other traditional fermented foods from Indonesia. Ann. Bogorienses V: 187-204.
  8. Steinkraus K. 1996. Handbook Indigenous Fermented Foods, 2nd Ed. Revised and expanded. Marcel Dekker Inc., New York NY.
  9. Atmodjo PK. 2006. Pengaruh variasi beras ketan (Oryza sativa var glutinosa L.) dan suhu fermentasi terhadap produksi alkohol. Biota 11: 152-158.
  10. Gandjar I, Slamet DS, Rukmi I. 1983. Brem Bali fermentation, pp. 26-28. In: Symposium on Research in Biology and Biotechnology in Developing Countries. November 2-4, National University of Singapore, Singapore.
  11. Gandjar I, Evrard P. 2002. Reidentification of the mycoflora in Ragi Tapai. Makara.
  12. Sujaya IN, Nocianitri KA, Asano K. 2010. Diversity of bacterial flora of Indonesian ragi tape and their dynamics during the tape fermentation as determined by PCR-DGGE. Int. Food Res. J. 17: 239-245.
  13. Hesseltine CW, Ray ML. 1988. Lactic acid bacteria in murcha and ragi. J. Appl. Bacteriol. 6: 395-401.
  14. Sujaya IN, Amachi S, Saito K, Yokota A, Asano K, Tomita F. 2002. Specific enumeration of lactic acid bacteria in ragi tape by colony hybridization with specific oligonucleotide probes. World J. Microbiol. Biotechnol. 17: 349-357.
  15. Muyzer G, Smalia K. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73: 127-141. https://doi.org/10.1023/A:1000669317571
  16. Water J, Tannock GW, Tilsala-Timisjarvi A, Rodtong S, Loach DM, Munro K, et al. 2000. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species specific PCR primer. Appl. Environ. Microbiol. 66: 297-303. https://doi.org/10.1128/AEM.66.1.297-303.2000
  17. Kim TW, Lee JH, Kim SE, Park MH, Chang HC, Kim HY. 2010. Analysis of microbial communities in doenjang, a Korean fermented soybean paste, using nested PCR-denaturing gradient gel electrophoresis. Int. J. Food Microbiol. 131: 265-271.
  18. Kim E, Cho Y, Lee Y, Han SK, Kim CG, Choo DW, et al. 2017. A proteomic approach for rapid identification of Weissella species isolated from Korean fermented foods on MALDI-TOF MS supplemented with an in-house database. Int. J. Food Microbiol. 243: 9-15. https://doi.org/10.1016/j.ijfoodmicro.2016.11.027
  19. Cho Y, Kim E, Lee Y, Han SK, Choo DW, Kim YR, et al. 2017. Rapid and accurate identification of Pediococcus species isolated from Korean fermented foods by MALDITOF MS with local database extension. Int. J. Syst. Evol. Microbiol. 67: 744-752. https://doi.org/10.1099/ijsem.0.001626
  20. Kwak HL, Han SK, Park S, Park SH, Shim JY, Oh MH, et al. 2015. Development of a rapid and accurate identification method for Citrobacter species isolated from pork products using matrix-assisted laser-desorption/ionization time-offlight mass spectrometry. J. Microbiol. Biotechnol. 25: 1537-1541. https://doi.org/10.4014/jmb.1503.03071
  21. Lane DJ. 1991. 16S/23S rRNA sequencing, pp. 115-175. In Stackebrandt E, Goodfellow M (eds.). Nucleic Acid Techniques in Bacterial Systematics. Wiley & Sons, New York, NY.
  22. Muyzer G, de Waal EC, Uitterlinden AG. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695-700.
  23. Vainio EJ, Hantula J. 2000. Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol Res. 104: 927-936. https://doi.org/10.1017/S0953756200002471
  24. Haruta S, Ueno S, Egawa I, Hashiguchi K, Fujii A, Nagano M, et al. 2006. Succession of bacterial and fungal communities during traditional pot fermentation of rice vinegar assessed by PCR-mediated denaturing gradient gel electrophoresis. Int. J. Food Microbiol. 109: 79-87. https://doi.org/10.1016/j.ijfoodmicro.2006.01.015
  25. Altschul SF, Madded TL, Schaffer AA, Zhang J, Zhang Z, Miller W. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. https://doi.org/10.1093/nar/25.17.3389
  26. Jung HJ, Hong Y, Yang HS, Chang HC, Kim HY. 2012. Distribution of lactic acid bacteria in garlic (Allium sativum) and green onion (Allium fistulosum) using SDS-PAGE wholecell protein pattern comparison and 16S rRNA gene sequence analysis. Food Sci. Technol. 21: 1457-1462.
  27. Pavlovic M, Newes A, Maggipinto M, Schmidt W, Messelhausser U, Balsliemke J, et al. 2014. MALDI-TOF MS based identification of food-borne yeast isolates. J. Microbiol. Methods 106: 123-128. https://doi.org/10.1016/j.mimet.2014.08.021
  28. Sujaya IN, Amachi S, Yokota A, Asano K, Tomita F. 2001. Identification and characterization of lactic acid bacteria in ragi tape. World J. Microbiol. Biotechnol. 18: 263-270.
  29. Ardhana MM, Fleet GH. 1989. The microbial ecology of tape ketan fermentation. Int. J. Food Microbiol. 9: 157-165. https://doi.org/10.1016/0168-1605(89)90086-X
  30. Yamada Y, Suzuki T, Matsuda M, Mikata K. 1995. The phylogeny of Yamadazyma ohmeri (Etchells et Bell) Billion-Grand based on the partial sequences of 18S and 26S ribosomal RNAs: the proposal of Kodamaea gen. nov. (Saccharomycetaceae). Biosci. Biotechnol. Biochem. 59: 1172-1174. https://doi.org/10.1271/bbb.59.1172
  31. Xiao Y, K ang M, T ang Y, Z ong Z, Zhang Y , He C , et al. 2013. Kodamaea ohmeri as an emerging pathogen in mainland China: 3 case reports and literature review. Lab. Med. 44: 1-9.
  32. Went FAFC, Geerligs HCP. 1895. Beobachtungen uber die hefearten and zuckerbildenden pilze der arackfabrikation. Verh. K. Akad. Wet. Amsterdam Ser. II 4: 3-31.
  33. Ellis JJ, Rhodes LJ, Hesseltine CW. 1976. The genus Amylomyces. Mycologia LXVIII: 131-143.
  34. Ayumi A, Sujaya N, Sone T, Asano K, Oda Y. 2004. Microflora and selected metabolites of potato pulp fermented with an Indonesian starter ragi tape. Food Technol. Biotechnol. 42: 169-173.
  35. Chiang YW, Chye FY, Mohd Ismail A. 2006. Microbial diversity and proximate composition of tapai, a Sabah's fermented beverage. Malays. J. Microbiol. 12: 1-6.

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