Phylogenomic analysis in Latilactobacillus sakei by using polymorphisms detected by next-generation sequencing
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Updated: Aug 4, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Chisato Nishiyama1, Suguru Sekiguchi2, Yu Sugihara3
1Laboratory of Plant Breeding, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-shi, Ishikawa 921-8836, Japan.
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.
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