Bioinformatic Analysis of the Genome of the Lactobacillus fermentum 90 TC-4 Production Strain

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At present, the Lactobacillus fermentum 90 TC-4 strain is widely used for production of probiotics, dietary supplements, and food. It is for this reason that it is topical to study this strain using modern molecular genetic methods. The biochemical properties of the strain were examined using the API 50 CHL test system (BioMerieux, France), genome sequencing was carried out using the MiSeq (Illumina) platform, and de novo genome assembly was performed using the Spades, MIRA 4.0, and Newbler 2.6 software. Genome annotation was carried out with the help of the Prokka v. 1.11 utility and RAST and BASys genomic servers. The main characteristics of the L. fermentum 90 TC-4 genome were established. It was proven that the genome does not have any determinants of pathogenicity, virulence or antibiotic resistance. It was shown that the low saccharolytic ability of the strain is associated with the absence of appropriate transport systems—the sucrose-specific phosphonolpyruvate system PTS_ScrA and ribose-specific RbsD permease—as well as several enzymes. The CRISPR-Cas locus of the strain was analyzed, unique spacers (which in future can be used for strain indication) were revealed, and molecular mechanisms of antibiotic resistance of the strain were studied. Using the MLST scheme presented in the scientific literature, allelic profiles of housekeeping genes were established. It was also found that the allelic profile obtained for the L. fermentum 90 TC-4 strain does not correspond to any of the previously described sequence types. Since L. fermentum 90 TC-4 does not have determinants of antibiotic resistance, pathogenicity, virulence, or integrated plasmids, the strain does not pose any hazard in terms of spread of these determinants and can be used as a probiotic producer strain. The observed features of the CRISPR locus and allelic profile can further be used to indicate the strain.

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Fig. 1.


  1. 1.

    Guidelines for the Control of Biological and Microbiological Factors. The System of Preregistration Preclinical Study of Drug Safety. Selection, Verification, and Storage of Production Strains Used in the Production of Probiotics: guidelines no. 4.2.2602-10, Moscow, Rospotrebnadzor, 2011.

  2. 2.

    Guidelines for the Sanitary-Epidemiological Assessment of the Safety and Functional Potential of Probiotic Microorganisms Used for Food Production: guidelines no., Moscow, Rospotrebnadzor, 2010.


  1. 1

    Lentsner, A.A., Some results of the study of human microflora lactobacilli, Materialy 5-oi konferentsii Tallinskogo nauchno-issledovatel’skogo instituta epidemiologii, mikrobiologii i gigieny (Proc. 5th Conference of Tallinn Scientific Research Institute of Epidemiology, Microbiology, and Hygiene), Tallinn, 1964.

  2. 2

    Platonov, M.E., Evseeva, V.V., Dentovskaya, S.V., and Anisimov, A.P., Molecular typing of Yersinia pestis, Mol. Genet.,Microbiol. Virol., 2013, vol. 28, no. 2, pp. 41–51.

  3. 3

    Horvatha, Ph., Coûté-Monvoisina, A.C., Romerob, D.A., Boyavala, P., Fremauxa, Ch., and Barrangoub, R., Comparative analysis of CRISPR loci in lactic acid bacteria genomes, Int. J. Food Microbiol., 2009, vol. 131, pp. 62–70.

  4. 4

    Hammes, W.P. and Hertel, C., The genus of Lactobacillus and Carnobacterium, Procaryotes, 2006, vol. 4, p. 320.

  5. 5

    Tarasova, N.B., Comparative study of lactobacilli and E. coli M-17 with the purpose of developing a new drug - Lactobacterin, Doctoral Sci (Med.) Dissertation, Gorki, 1969.

  6. 6

    Seemann, T., Prokka: Rapid prokaryotic genome annotation, Bioinformatics, 2014, vol. 30, pp. 2068–2069.

  7. 7

    Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., et al., The RAST server: Rapid Annotations using Subsystems Technology, BMC Genomics, 2008, vol. 8, p. 75.

  8. 8

    Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., et al., Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother., 2012, vol. 67, pp. 2640–2644.

  9. 9

    Cosentino, S., Voldby, L.M., Møller, A.F., and Lund, O., PathogenFinder distinguishing friend from foe using bacterial whole genome sequence data, PLoS One, 2013, vol. 8, no. 10, p. e77302.

  10. 10

    Grissa, I., Vergnaud, G., and Pourcel, K., The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats, BMC Bioinf., 2007, vol. 8, no. 1, p. 172.

  11. 11

    Dan, T., Liu, W., Yuqin Song, Y., Xu, H., Menghe, B., Zhang, H., and Sun, Z., The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST), BMC Microbiol., 2015, vol. 15, p. 107.

  12. 12

    Solov’eva, I.V., Tochilina, A.G., Belova, I.V., Efimov, E.I., Novikova, N.A., and Ivanova, T.P., Construction of an immobilized form of the liquid probiotic, Vestn. Nizhegorod. Lobachevskogo, 2012, vol. 2, pp. 85–92.

  13. 13

    Sidorenko, S.V. and Tishkov, V.I., Molecular bases of antibiotic resistance, Usp. Biol. Khim., 2004, vol. 44, pp. 263–306.

  14. 14

    Hummel, A.S., Hertel, C., Holzapfel, W.H., Charles, M., and Franz, A.P., Antibiotic resistances of starter and probiotic strains of lactic acid bacteria, Appl. Environ. Microbiol., 2007, vol. 73, p. 730.

  15. 15

    Shashkova, A.V., Goryaev, A.A., and Smirnova, N.I., Structure and functional role of bacterial CRISPR system, Probl. Osobo Opasnykh Infekts., 2011, vol. 2, pp. 49–52.

  16. 16

    Makarova, K.S., Wolf, H., Alkhnbashi, O.S., Costa, F., Shah, S.A., Saunders, S.J., et al., An updated evolutionary classification of CRISPR-Cas systems, Nat. Rev. Microbiol., 2015, vol. 13, pp. 722–736.

  17. 17

    Viktorov, D.V. and Piven’, N.N., Active membrane transport and multiple antibiotic resistance of bacteria, Mol. Genet., Mikrobiol. Virusol., 2001, vol. 3, pp. 3–8.

  18. 18

    Devirgiliis, C., Zinno, P., and Perozzi, G., Update on antibiotic resistance in foodborne Lactobacillus and Lactococcus species, Front. Microbiol., 2013, vol. 4, p. 301.

  19. 19

    Stefanovic, E., Fitzgerald, G., and McAuliffe, O., Advances in the genomics and metabolomics of dairy lactobacilli: A review, Food Microbiol., 2017, vol. 61, p. 33.

  20. 20

    Barrangou, R. and Dudley, E.G., CRISPR-based typing and next-generation tracking, Annu. Rev. Food Sci. Technol., 2016, vol. 7, pp. 395–411.

  21. 21

    Antonov, V.A., Altukhova, V.V., Savchenko, S.S., Zamaraev, V.S., Ilyukhin, V.I., and Alekseev, V.V., The use of multilocus sequence typing (MLST) and randomly amplified polymorphic DNA (RAPD) to differentiate among strains of the glanders pathogen Burkholderia mallei, Mol. Genet.,Microbiol. Virol., 2007, vol. 22, no. 3, pp. 87–94.

  22. 22

    Kuznetsova, T.V., Kebekbaeva, K.M., Dzhakibaeva, G.T., and Molzhigitova, A.E., Genotyping of lactic acid bacteria strains by PCR, Sovrem. Probl. Nauki Obraz., 2016, no. 5. view?id=25349. Accessed November 13, 2017.

  23. 23

    Shurkhno, R.A., Vologin, S.G., Gibadullina, F.S., and Tagirov, M.Sh., Screening of natural strains of lactic acid bacteria and their taxonomic identification, 2015, no. 2. id=21189. Accessed November 13, 2017.

  24. 24

    Shevtsov, A.B., Kushugulova, A.R., Tynybaeva, I.K., Kozhakhmetov, S.S., Abzhalelov, A.B., Momynaliev, K.T., and Stoyanova, L.G., Identification of phenotypically and genotypically related Lactobacillus strains based on nucleotide sequence analysis of the groEL, rpoB, rplB, and 16S rRNA genes, Microbiology (Moscow), 2011, vol. 80, no. 5, pp. 672–681.

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Correspondence to A. G. Tochilina.

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The authors declare that they have no conflict of interest.

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Translated by K. Lazarev

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Tochilina, A.G., Belova, I.V., Soloveva, I.V. et al. Bioinformatic Analysis of the Genome of the Lactobacillus fermentum 90 TC-4 Production Strain. Mol. Genet. Microbiol. Virol. 34, 176–181 (2019) doi:10.3103/S0891416819030078

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  • Lactobacillus fermentum
  • genome-wide sequencing
  • bioinformatic analysis
  • sugar metabolism genes
  • CRISPR locus