Genetic and epigenetic diversity in cheese starter culture lactic acid bacteria

Strain-level diversity among lactic acid bacteria in cheese starter cultures critically shapes fermentation outcomes, yet the genetic and epigenetic mechanisms underpinning this diversity remain underexplored. Here, we perform comprehensive genome and methylome profiling of 41 strains from mesophilic cheese starter cultures using Oxford Nanopore sequencing. Despite high genomic similarity (average nucleotide identity >99% within species), strains exhibited distinct DNA methylation signatures driven by diverse restriction-modification (R-M) systems.