Skip to main content
SpringerLink
Log in

Phenotypic and genotypic identification of lactic acid bacteria isolated from traditional pickles of the Çubuk region in Turkey

  • Published:
Folia Microbiologica Aims and scope Submit manuscript

Abstract

A total of 152 lactic acid bacteria (LAB) were isolated from pickles produced in the Ankara-Çubuk region. These isolates were clustered into eight groups on the basis of their phenotypic characteristics including cell morphology, CO2 production from glucose, growth at 10 and 45 °C, growth in 6.5 % NaCl, and growth at pH 9.6. API 50 CH carbohydrate fermentation test, 16S ribosomal RNA (rRNA) sequence analysis, and sodium dodecyl sulfate-acrylamide gel electrophoresis (SDS-PAGE) whole-cell protein profile analysis were also performed for precise identification of the isolates at the species level. Molecular identification revealed that the most prevalent LAB species involved in pickle fermentation were Pediococcus ethanolidurans (46 isolates, 30.3 %), Lactobacillus brevis (37 isolates, 24.3 %), Lactobacillus plantarum (37 isolates, 24.3 %), and Lactobacillus buchneri (15 isolates, 9.9 %). Other LAB were found in minor frequencies such as Pediococcus parvulus (8 isolates, 5.3 %), Lactobacillus namurensis (6 isolates, 3.9 %), Lactobacillus diolivorans (1 isolate, 0.7 %), Lactobacillus parabrevis (1 isolate, 0.7 %), and Enterococcus casseliflavus (1 isolate, 0.7 %). When results of phenotypic and genotypic identification methods were compared, differences in the species distribution of LAB associated with pickles were defined between the API and the 16S rRNA sequencing. The API 50 CHL test coincided with the 16S rRNA results in 71 out of the 152 tested isolates, indicating that API gave unreliable identification results. A clear correlation could not be found between the results of whole-cell SDS profiles and 16S rRNA sequencing. Therefore, molecular characterization by 16S rRNA sequencing was considered to be the most reliable method for identifying isolates. The results presented in this work provide insight in to the LAB population associated with traditional Çubuk pickles and constitute a LAB strain resource for further studies involving the development of starter cultures.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig 1

Similar content being viewed by others

References

  • Axelsson L (2004) Lactic acid bacteria: classification and physiology. In: Salminen S, von Wright A, Ouwehand A (eds) Lactic acid bacteria: microbiological and functional aspects, 3rd edn. Marcel Dekker, New York

    Google Scholar 

  • Balcázar JL, de Blas I, Ruiz-Zarzuela I, Vendrell D, Gironés O, Muzquiz JL (2007) Sequencing of variable regions of the 16S rRNA gene for identification of lactic acid bacteria isolated from the intestinal microbiota of healthy salmonids. Comp Immunol Microbiol Infect Dis 30:111–118

    Article  PubMed  Google Scholar 

  • Boyd MA, Antonio MAD, Hillier SL (2005) Comparison of API 50 CH strips to whole-chromosomal DNA probes for identification of Lactobacillus species. J Clin Microbiol 43(10):5309–5311

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Breidt F, Medina E, Wafa D, Pérez-Díaz I, Franco W, Huang H-Y, Johanningsmeier SD, Kim JH (2013) Characterization of cucumber fermentation spoilage bacteria by enrichment culture and 16S rDNA cloning. J Food Sci 78(3):M470–M476

    Article  CAS  PubMed  Google Scholar 

  • Çetin B (2011) Production of probiotic mixed pickles (Turşu) and microbiological properties. Afr J Biotechnol 10(66):14926–14931

    Article  Google Scholar 

  • Chao S-H, Wu R-J, Watanabe K, Tsai Y-C (2009) Diversity of lactic acid bacteria in suan-tsai and fu-tsai, traditional fermented mustard products of Taiwan. Int J Food Microbiol 135:203–210

    Article  PubMed  Google Scholar 

  • Chen Y, Wu H, Lo H, Lin W, Hsu W, Lin C, Lina P, Yanagida F (2012) Isolation and characterisation of lactic acid bacteria from jiang-gua (fermented cucumbers), a traditional fermented food in Taiwan. J Sci Food Agric 92:2069–2075

    Article  CAS  PubMed  Google Scholar 

  • Çon AH, Karasu N (2009) Determination of antagonistic starter cultures for pickle and olive fermentation processes. Czech J Food Sci 27(3):185–193

    Google Scholar 

  • De Angelis M, Corsetti A, Tosti N, Rossi J, Corbo MR, Gobbetti M (2001) Characterization of Non-starter lactic acid bacteria from Italian ewe cheeses based on phenotypic, genotypic, and cell wall protein analyses. Appl Environ Microbiol 67(5):2011–2020

    Article  PubMed Central  PubMed  Google Scholar 

  • Endo A, Mizuno H, Okada S (2008) Monitoring the bacterial community during fermentation of sunki, an unsalted, fermented vegetable traditional to the Kiso area of Japan. Lett Appl Microbiol 47:221–226

    Article  CAS  PubMed  Google Scholar 

  • Franco W, Pérez-Díaz IM (2012) Role of selected oxidative yeasts and bacteria in cucumber secondary fermentation associated with spoilage of the fermented fruit. Food Microbiol 32:338–344

    Article  CAS  PubMed  Google Scholar 

  • Franco W, Pérez-Díaz IM, Johanningsmeier SD, McFeeters RF (2012) Characteristics of spoilage-associated secondary cucumber fermentation. Appl Environ Microbiol 78(4):1273–1284

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hammes WP, Hertel C (2006) The genera Lactobacillus and Carnobacterium. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The Prokaryotes A Handbook on the Biology of Bacteria, 3rd edn. Springer Science + Business Media, New York, pp 320–403

    Google Scholar 

  • Hitchener BJ, Egan AF, Rogers PJ (1982) Characteristics of lactic acid bacteria isolated from vacuum-packaged beef. J Appl Bacteriol 52(1):31–37

    Article  CAS  PubMed  Google Scholar 

  • Hutkins RW (2006) Microbiology and technology of fermented foods. Blackwell Publishing, USA

    Book  Google Scholar 

  • Iuchi A, Haruguchi S, Mongkolthanaruk W, Arima J, Nagase M, Khanh HQ, Ichiyanagi T, Yamaguchi T, Shimomura N, Aimi T (2012) Characterization of novel amylase from amylolytic lactic acid bacteria Pediococcus ethanolidurans isolated from Japanese pickles (nuka-zuke). Food Sci Technol Res 18(6):861–867

    Article  CAS  Google Scholar 

  • Johanningsmeier SD, McFeeters RF (2013) Metabolism of lactic acid in fermented cucumbers by Lactobacillus buchneri and related species, potential spoilage organisms in reduced salt fermentations. Food Microbiol 35:129–135

    Article  CAS  PubMed  Google Scholar 

  • Kabak B, Dobson ADW (2011) An introduction to the traditional fermented foods and beverages of Turkey. Crit Rev Food Sci Nutr 51:248–260

    Article  PubMed  Google Scholar 

  • Kato K, Toh H, Sakamoto N, Mori K, Tashiro K, Hibi N, Sonomoto K, Nakayamaa J (2014) Draft genome sequence of Lactobacillus namurensis Chizuka 01, isolated from nukadoko, a pickling bed of fermented rice bran. Genome Announc 2(1):e01263–13. doi:10.1128/genomeA. 01263-13

    PubMed Central  PubMed  Google Scholar 

  • Kim S-Y, Adachi Y (2007) Biological and genetic classification of canine intestinal lactic acid bacteria and bifidobacteria. Microbiol Immunol 51(10):919–928

    Article  CAS  PubMed  Google Scholar 

  • Kingston JJ, Radhika M, Roshini PT, Raksha MA, Murali HS, Batra HV (2010) Molecular characterization of lactic acid bacteria recovered from natural fermentation of beet root and carrot Kanji. Indian J Microbiol 50:292–298

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kizerwetter-Swida M, Binek M (2005) Selection of potentially probiotic Lactobacillus strains towards their inhibitory activity against poultry enteropathogenic bacteria. Pol J Microbiol 54(4):287–294

    CAS  PubMed  Google Scholar 

  • Krooneman J, Faber F, Alderkamp AC, Elferink SJHWO, Driehuis F, Cleenwerck I, Swings J, Gottschal JC, Vancanneyt M (2002) Lactobacillus diolivorans sp. nov., a 1,2-propanediol-degrading bacterium isolated from aerobically stable maize silage. Int J Syst Evol Microbiol 52:639–646

    CAS  PubMed  Google Scholar 

  • Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685

    Article  CAS  PubMed  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley and Sons, Chichester, pp 115–147

    Google Scholar 

  • Liu L, Zhang B, Tong H, Dong X (2006) Pediococcus ethanolidurans sp. nov., isolated from the walls of a distilled-spirit-fermenting cellar. Int J Syst Evol Microbiol 56:2405–2408

    Article  CAS  PubMed  Google Scholar 

  • Markiewicz LH, Biedrzycka E, Wasilewska E, Bielecka M (2010) Rapid molecular identification and characteristics of Lactobacillus strains. Folia Microbiol 55(5):481–488

    Article  CAS  Google Scholar 

  • Moraes PM, Perin LM, Júnior AS, Nero LA (2013) Comparison of phenotypic and molecular tests to identify lactic acid bacteria. Braz J Microbiol 44(1):109–112

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pogačić T, Kelava N, Zamberlin Š, Dolenčić-Špehar I, Samaržija D (2010) Methods for culture-independent identification of lactic acid bacteria in dairy products. Food Technol Biotechnol 48(1):3–10

    Google Scholar 

  • Pot B, Ludwig W, Kersters K, Schleifer K-H (1994) Taxonomy of lactic acid bacteria. In: De Vuyst L, Vandamme EJ (eds) Bacteriocins of lactic acid bacteria. Microbiology, genetics and applications. Springer Science + Business Media, New York, pp 13–90

    Chapter  Google Scholar 

  • Randazzo CL, Restuccia C, Romano AD, Caggia C (2004) Lactobacillus casei, dominant species in naturally fermented Sicilian green olives. Int J Food Microbiol 90:9–14

    Article  PubMed  Google Scholar 

  • Reina LD, Breidt F Jr, Fleming HP, Kathariou S (2005) Isolation and selection of lactic acid bacteria as biocontrol agents for nonacidified, refrigerated pickles. J Food Sci 70(1):M7–M11

    Article  CAS  Google Scholar 

  • Sakamoto N, Tanaka S, Sonomoto K, Nakayama J (2011) 16S rRNA pyrosequencing-based investigation of the bacterial community in nukadoko, a pickling bed of fermented rice bran. Int J Food Microbiol 144:352–359

    Article  CAS  PubMed  Google Scholar 

  • Sánchez I, Palop L, Ballesteros C (2000) Biochemical characterization of lactic acid bacteria isolated from spontaneous fermentation of ‘Almagro’ eggplants. Int J Food Microbiol 59:9–17

    Article  PubMed  Google Scholar 

  • Sánchez I, Seseña S, Palop LL (2004) Polyphasic study of the genetic diversity of lactobacilli associated with ‘Almagro’ eggplants spontaneous fermentation, based on combined numerical analysis of randomly amplified polymorphic DNA and pulsed-field gel electrophoresis patterns. J Appl Microbiol 97:446–458

    Article  PubMed  Google Scholar 

  • Scheirlinck I, Meulen RV, Schoor AV, Cleenwerck I, Huys G, Vandamme P, Vuyst LD, Vancanneyt M (2007) Lactobacillus namurensis sp. nov., isolated from a traditional Belgian sourdough. Int J Syst Evol Microbiol 57:223–227

    Article  CAS  PubMed  Google Scholar 

  • Schillinger U, Holzapfel WH (1995) The genus Carnobacterium. In: Wood BJB, Holzapfel WH (eds) The genera of lactic acid bacteria, 1st edn. Chapman & Hall, UK, pp 307–324

    Chapter  Google Scholar 

  • Simpson WJ, Taguchi H (1995) The genus Pediococcus, with notes on the genera Tetratogenococcus and Aerococcus. In: Wood BJB, Holzapfel WH (eds) The genera of lactic acid bacteria, 1st edn. Chapman & Hall, UK, pp 125–172

    Chapter  Google Scholar 

  • Şimşek Ö, Çon AH, Tulumoğlu Ş (2006) Isolating lactic starter cultures with antimicrobial activity for sourdough processes. Food Control 17:263–270

    Article  Google Scholar 

  • Singh AK, Ramesh A (2008) Succession of dominant and antagonistic lactic acid bacteria in fermented cucumber: insights from a PCR-based approach. Food Microbiol 25:278–287

    Article  CAS  PubMed  Google Scholar 

  • Tamang JP, Tamang B, Schillinger U, Franz CMAP, Gores M, Holzapfel WH (2005) Identification of predominant lactic acid bacteria isolated from traditionally fermented vegetable products of the Eastern Himalayas. Int J Food Microbiol 105:347–356

    Article  CAS  PubMed  Google Scholar 

  • Tamminen M, Joutsjoki T, Sjöblom M, Joutsen M, Palva A, Ryhänen E-L, Joutsjoki V (2004) Screening of lactic acid bacteria from fermented vegetables by carbohydrate profiling and PCR–ELISA. Lett Appl Microbiol 39:439–444

    Article  CAS  PubMed  Google Scholar 

  • Temmerman R, Huys G, Swings J (2004) Identification of lactic acid bacteria: culture-dependent and culture-independent methods. Trends Food Sci Technol 15:348–359

    Article  CAS  Google Scholar 

  • Vancanneyt M, Naser SM, Engelbeen K, Wachter MD, Meulen RV, Cleenwerck I, Hoste B, Vuyst LD, Swings J (2006) Reclassification of Lactobacillus brevis strains LMG 11494 and LMG 11984 as Lactobacillus parabrevis sp. nov. Int J Syst Evol Microbiol 56:1553–1557

    Article  CAS  PubMed  Google Scholar 

  • Vandamme P, Pot B, Gillis M, De Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematic. Microbiol Rev 60(2):407–438

    PubMed Central  CAS  PubMed  Google Scholar 

  • Xiong T, Guan Q, Song S, Hao M, Xie M (2012) Dynamic changes of lactic acid bacteria flora during Chinese sauerkraut fermentation. Food Control 26:178–181

    Article  CAS  Google Scholar 

  • Yu J, Gao W, Qing M, Sun Z, Wang W, Liu W, Pan L, Sun T, Wang H, Bai N, Zhang H (2012) Identification and characterization of lactic acid bacteria isolated from traditional pickles in Sichuan, China. J Gen Appl Microbiol 58:163–172

    Article  CAS  PubMed  Google Scholar 

  • Zhang C, Brandt MJ, Schwab C, Gänzle MG (2010) Propionic acid production by cofermentation of Lactobacillus buchneri and Lactobacillus diolivorans in sourdough. Food Microbiol 27:390–395

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research was supported by the Scientific and Technological Research Council of Turkey (Project No. 108O491).

Author information

Authors and Affiliations

  1. Faculty of Engineering, Department of Food Engineering, Ankara University, Ankara, Turkey

    Simel Bağder Elmacı & Filiz Özçelik

  2. Faculty of Natural Sciences and Engineering, Department of Food Engineering, Gaziosmanpaşa University, Tokat, Turkey

    Mehmet Tokatlı

  3. Faculty of Engineering, Department of Food Engineering, Gaziantep University, Gaziantep, Turkey

    Derya Dursun

  4. Kalecik Vocational School, Food Technology Program, Ankara University, Ankara, Turkey

    Pınar Şanlıbaba

Authors
  1. Simel Bağder Elmacı
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mehmet Tokatlı
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Derya Dursun
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Filiz Özçelik
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Pınar Şanlıbaba
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Simel Bağder Elmacı.

Additional information

Simel Bağder Elmacı and Mehmet Tokatlı contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bağder Elmacı, S., Tokatlı, M., Dursun, D. et al. Phenotypic and genotypic identification of lactic acid bacteria isolated from traditional pickles of the Çubuk region in Turkey. Folia Microbiol 60, 241–251 (2015). https://doi.org/10.1007/s12223-014-0363-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12223-014-0363-x

Keywords

Search

Navigation