Genomic and transcriptomic analyses of ropy slime producing Latilactobacillus sakei reveal a specific exopolysaccharide cluster with temperature-dependent transcription activity

Latilactobacillus sakei is a psychrotrophic lactic acid bacterium (LAB) with a wide genomic diversity. It is mainly associated with food fermentation, but some strains can spoil meat products by generation of ropy exopolysaccharide (EPS). Despite the important role of L. sakei in foods, virtually nothing was known about the gene cluster related to the formation of ropy EPS or how temperature affected its expression. Furthermore, no experimental in vitro model system for experimenting with EPS production was available. The ability to form ropy EPS has been evaluated either with an inoculation study or testing the ropiness of a colony. To address these limitations, we (I) sequenced the genomes of 59 L. sakei strains, (II) characterized their EPS gene clusters and performed comparative genomic and phylogenetic analyses, (III) developed an in vitro model system for EPS production and (IV) tested the effect of temperature on EPS production using transcriptomic analysis of RNA-seq data from a longitudinal growth experiment at 10 °C and 30 °C. Genomic analyses showed showed the existence of one phylogenetically highly similar group of strains. Characterisation of the EPS gene cluster revealed that it differs from known bacterial EPS clusters in that it lacks separate epsB and epsC genes. Temperature had a noticeable effect on EPS production, with strong ropy EPS production at 10 °C whereas no visible EPS was detected at 30 °C. Transcriptomic analyses revealed differences in the EPS cluster activity, with the first half of the cluster being more active at 10 °C and the second half at 30 °C.