Sulistiani Sulistiani, Wibowo Mangunwardoyo, Abinawanto Abinawanto, Endang Sukara, Achmad Dinoto, Andi Salamah
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Molecular analysis of Lactobacillus fermentum isolates is essential to understand their genetic variation in relations to their roles in sayur asin fermentation process. Combination of three molecular techniques which is restriction fragment length polymorphism (RFLP) of 16S23S rDNA intergenic spacer region (ISR), random amplified polymorphic DNA (RAPD-PCR) and an enterobacterial repetitive intergenic consensus (ERIC-PCR) analysis were performed to discriminate 19 representative isolates of L. fermentum isolated from sayur asin. The result showed that L. fermentum strain D11 is distantly related to other isolates based on RFLP using HhaI restriction enzyme and RAPDPCR analyses. In addition, both of RAPD-PCR and ERIC-PCR successfully determined the genetic variation among L. fermentum strains by exhibiting distinct 4-8 bands (800-2080 bp) and 4-10 bands (280-3050 bp), respectively. A dendogram generated from UPGMA cluster analysis of both RAPD-PCR and ERIC-PCR data showed two distinct genotypic groups exist among L. fermentum isolated from sayur asin in Indonesia.


ERIC-PCR, genetic variation, Lactobacillus fermentum, RAPD-PCR, RFLP 16S-23S rDNA, ISR.

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Belgacem, Z.B., Dousset, X., Prevost, H. and Manai, M., 2009. Polyphasic taxonomic studies of lactic acid bacteria associated with tunisian fermented meat based on the heterogeneity of the 16S-23S rRNA gene intergenic spacer region. Archives of Microbiology, 191, pp. 711-720.

Daeschel, M.A., Andersson, R.E. and Fleming, H.P., 1987. Microbial ecology of fermenting plant material. FEMS Microbiology Reviews, 46, pp. 357-367.

Franco, M., Quintana, A., Duque, C., Suarez, C., Rodriguez, M.X. and Barea, J., 2010. Evaluation of actinomycetes strains for key traits related with plant growth promotion and mycorrhiza helping activities. Applied Soil Ecology, 45, pp. 209-217.

Gillings, M. and Holley, M., 1997. Repetitive element PCR fingerprinting (rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC) primers is not necessarily directed at ERIC elements. Letter in Applied Micro-biology, 25, pp.17-21.

Gurtler, V. and Stanisich, V.A., 1996. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology, 142, pp. 3-16.

Huey, B. and Hall, J., 1989. Hypervariable DNA fingerprinting in Eschericia coli: minisatelite probe from bacteriophage M13. Journal of Bacteriology, 171(5), pp. 2528-2532.

Miteva, V., Boudakov, I.,Toyancheva, G.I.S., Marinova, B., Mitev V. and Mengaud, J., 2001. Differentiation of Lactobacillus delbrueckii subspecies by ribotyping and amplified ribosomal DNA restriction analysis (ARDRA). Journal of Applied Microbiology, 90, pp. 909-918.

Moschetti, G., Blaiotta, G., Aponte, M., Catzeddu, P., Villani, F., Deiana, P. and Coppola, S., 1998. Random amplified polymorphic DNA and amplified ribosomal DNA spacer polymorphism: powerful methods to differentiate Streptococcus thermophilus strains. Journal of Applied Microbiology, 85(1), pp. 25-36.

Nei, M. and Li, W., 1979. Mathematical model for studying gen-etic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America. 76(10), pp.5269-5273.

Promega. 2012. Certificate of Analysis GoTaq® Green Master Mix and Usage Information. Part# 9PIM712 and Revised 3/12. (Diunduh 11Mei 2014).

Puspito, H. and Fleet, G.H., 1985. Microbiology of sayur asin fermentation. Applied Microbiology and Biotechnology, 22, pp.442-445.

Rachman, C.N., Kabadjova, P., Prévost H. and Dousset. X., 2003. Identification of Lactobacillus alimentarius and Lactobacillus farciminis with 16S-23S rDNA intergenic spacer region polymorphism and PCR amplification using species-specific oligonucleotide. Journal of Applied Microbiology, 95, pp.1207-1216.

Rivas, B., Marcobal, ?. and Munoz, R., 2006. Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains. Microbiology, 152, pp. 85-93.

Rohlf, F.J., 1998. NTSYS/PC numerical taxonomy and multivariate analysis system. Version 2.0. Applied Biostatistics Inc, New York.

Rossetti, L. and Giraffa, G., 2005. Rapid identification of dairy lactic acid bacteria by M 13-generated, RAPD-PCR fingerprint databases. Journal of Microbiological Methods, 63, pp.135-144.

Saito S., Kobayashi, M., Kimoto-Nira, H., Aoki, R., Mizumachi, K., Miyata, S., Yamamoto, K., Kitagawa, Y. and Suzuki. C., 2011. Intraspecies Discrimination of Lactobacillus paraplantarum by PCR. FEMS Microbiology Letters, 316, pp. 70-76.

Solieri, L., Genova, F., De Paola, M. and Giudici, P., 2009. Characterization and technological properties of Oenococcus oeni strains from wine spontaneous malolactic fermentations: A Framework for selection of new starter cultures. Journal of Applied Microbiology, 108, pp. 285-298.

Sulistiani, Abinawanto, Sukara, E., Salamah, A., Dinoto A. and Mangunwardoyo, W., 2014. Identification of lactic acid bacteria in sayur asin from central java (Indonesia) based on 16S rDNA sequence. International Food Research Journal, 21(2), pp. 527-532.

Yavuz, E., Gunes, H., Bulut, C., Harsa, S. and Yenidunya, A.F., 2004. RFLP of 16S-ITS rDNA Region to differentiate lactobacilli at species level. World Journal of Microbiology and Biotechnology, 20(6), pp. 535-537.

Zavaleta, A.I., Murcia, A.J.M. and Valera, F.R., 1996. 16S-23S rDNA Intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous. Microbiology, 142, pp. 2105-2114.

Zulkifli, Y., Alitheen, N.B., Son, R., Raha, A.R., Samuel, L., Yeap, S.K. and Nishibuchi, M., 2009. Random amplified polymorphic DNA-PCR and ERIC PCR analysis on Vibrio parahaemolyticus isolated from cockles in Padang, Indonesia. International Food Research Journal, 16, pp. 141-150.


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