Bioinformatic analysis of the genome Lactobacillus fermentum 90 TC-4 production strain

Tochilina A.G.

Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia, 603000

Belova I.V.

Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia, 603000

Solovieva I.V.

JSC DIAKON, Pushchino, Moscow region, Russia

Ivanova T.P.

Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia, 603000

Zhirnov V.A.

Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia, 603000

Bioinformatic analysis of the genome Lactobacillus fermentum 90 TC-4 production strain

Authors:

Tochilina A.G., Belova I.V., Solovieva I.V., Ivanova T.P., Zhirnov V.A.

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Journal: Molecular Genetics, Microbiology and Virology. 2019;37(3): 128‑133

DOI: 10.17116/molgen201937031128

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Tochilina AG, Belova IV, Solovieva IV, Ivanova TP, Zhirnov VA. Bioinformatic analysis of the genome Lactobacillus fermentum 90 TC-4 production strain. Molecular Genetics, Microbiology and Virology. 2019;37(3):128‑133. (In Russ.)
https://doi.org/10.17116/molgen201937031128

Подписка 2025-2 (Molecular Genetics, Microbiology and Virology)

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At present, Lactobacillus fermentum 90 TC-4 strain is widely used for production of probiotics, dietary supplements and food. This justifies the relevance of strain study using modern molecular-genetic methods. Biochemical properties of the strain were examined using the API 50 CHL test system («BioMerieux», France), genome sequencing was performed on the MiSeq («Illumina») platform, de novo genome assembly was performed using Spades, MIRA 4.0 and Newbler 2.6 programs. Genome annotation was perfomed with the help of Prokka v. 1.11. utility and RAST and BASys genomic servers. The main characteristics of L. fermentum 90 TC-4 genome have been established. It has been proved that the genome doesn’t have any pathogenicity, virulence or antibiotic resistance determinants. It has been shown that the low saccharolytic capacity of the strain is associated with the absence of appropriate transport system — PTS_ScrA and RbsD permease system specific for ribose as well as a number of enzymes. The CRISPR-Cas locus of the strain has been analyzed, unique spacers (which in future can be used for strain indication) have been revealed, molecular mechanisms of strain antibiotic resistance have been studied. Using the MLST scheme, presented in the scientific literature, allelic profiles of housekeeping genes have been established. It has been established that the allelic profile, obtained for L. fermentum 90 TC-4 strain, does not correspond to any of the previously described sequence-types. D 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 propagation of these determinants and can be used as a probiotic producer strain. The observed features of CRISPR locus and allelic profile can further be used to indicate the strain.

Keywords:

Lactobacillus fermentum

probiotic strains

full genomic sequencing

bioinformatic analysis

sugar metabolism genes

CRISPR locus

Authors:

Tochilina A.G.

Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia, 603000

Belova I.V.

Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia, 603000

Solovieva I.V.

JSC DIAKON, Pushchino, Moscow region, Russia

Ivanova T.P.

Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia, 603000

Zhirnov V.A.

Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Russia, 603000

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