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

Area of Science:

• Microbiology
• Genomics
• Food Science

Background:

• Latilactobacillus sakei is a key lactic acid bacterium utilized in diverse fermented food production.
• Understanding L. sakei adaptability to various nutrient sources is crucial for optimizing fermentation processes.

Purpose of the Study:

• To perform phylogenetic analysis of 32 L. sakei strains using a novel sequence-based method.
• To investigate the primary drivers of phylogenetic relationships in L. sakei, specifically nutrition sources versus geographical origin.

Main Methods:

• Whole-genome sequencing was employed to identify polymorphisms within L. sakei strains.
• Strain-specific, nucleotide-concatenated (SSC) sequences were generated by combining these polymorphisms.
• Phylogenetic analysis was conducted using the developed SSC sequences for 32 L. sakei isolates.

Main Results:

• SSC sequence analysis provided a robust method for phylogenetic inference, avoiding biases associated with partial sequence selection.
• The phylogenetic relationships among L. sakei strains were predominantly determined by their diverse nutrition sources.
• Geographical location did not emerge as a significant factor influencing the evolutionary pathways of L. sakei.

Conclusions:

• Phylogenetic relationships in L. sakei are primarily shaped by adaptation to different nutrient environments.
• The SSC sequencing approach offers a powerful tool for high-resolution phylogenetic studies in bacteria.
• Findings provide insights into the ecological adaptability of L. sakei, relevant for food fermentation applications.