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Phylogenomic analysis in Latilactobacillus sakei by using polymorphisms detected by next-generation sequencing.

ABSTRACT: Latilactobacillus sakei is a lactic acid bacterium used to produce a wide range of fermented food products. To understand their characteristics and adaptability to various nutrient sources, we applied strain-specific, nucleotide-concatenated (SSC) sequences to the phylogenetic analysis of 32 L. sakei strains isolated from various locations and products. SSC sequences were developed by concatenating the polymorphisms detected by whole-genome sequencing. This enabled us to use sufficient polymorphisms and avoid the bias caused by selecting partial sequences, such as that in core genome and multi-locus sequence typing. SSC sequence-based analysis revealed that the phylogenetic relations for L. sakei are based on the different nutrition sources rather than geographical distance.

SUBMITTER: Nishiyama C

PROVIDER: S-EPMC10067329 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Phylogenomic analysis in Latilactobacillus sakei by using polymorphisms detected by next-generation sequencing.

Nishiyama Chisato C Sekiguchi Suguru S Sugihara Yu Y Nishikawa Minami M Makita Natsu N Segawa Tenta T Terasaki Momoka M Takagi Hiroki H Koyanagi Takashi T

Bioscience of microbiota, food and health 20230113 2

Latilactobacillus sakei is a lactic acid bacterium used to produce a wide range of fermented food products. To understand their characteristics and adaptability to various nutrient sources, we applied strain-specific, nucleotide-concatenated (SSC) sequences to the phylogenetic analysis of 32 L. sakei strains isolated from various locations and products. SSC sequences were developed by concatenating the polymorphisms detected by whole-genome sequencing. This enabled us to use ...[more]

PMID: 37016685

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