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

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. sake...

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Bibliographic Details
Published in:Bioscience of Microbiota, Food and Health Food and Health, 2023, pp.2022-017
Main Authors: NISHIYAMA, Chisato, SEKIGUCHI, Suguru, SUGIHARA, Yu, NISHIKAWA, Minami, MAKITA, Natsu, SEGAWA, Tenta, TERASAKI, Momoka, TAKAGI, Hiroki, KOYANAGI, Takashi
Format: Article
Language:English
Subjects:
Adaptability
Fermented food
Gene sequencing
Genomes
Lactic acid
Latilactobacillus sakei
Multilocus sequence typing
Next-generation sequencing
next-generation sequencing (NGS)
Nucleotide sequence
Nucleotides
Nutrient sources
phylogenomic analysis
Phylogeny
Whole genome sequencing
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Summary: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.
ISSN:2186-3342
2186-6953
2186-3342
DOI:10.12938/bmfh.2022-017