Comparative Genomics of Fermented Vegetable-Derived Leuconostoc mesenteroides from Biodiversity Hotspot Yunnan, China

Fermented vegetables in Yunnan Province, China, harbor abundant microbial diversity. However, the development of indigenous starter cultures remains under-utilized. Genomic information regarding Leuconostoc (L.) mesenteroides isolates from this region is particularly scarce. To assess the genomic characteristics of eight L. mesenteroides isolates from traditional Yunnan fermented vegetables, we performed whole-genome sequencing and conducted a comparative analysis with 21 publicly available vegetable-derived genomes. Comparative genomic analysis revealed marked variation in genome size and plasmid content, and pangenome analysis indicated an open configuration. Core-genome multilocus sequence typing (cgMLST) of the eight indigenous isolates showed high allelic diversity, indicating a genetically heterogeneous and non-clonal population. Phylogenomic analysis revealed that the evolutionary relationships among the 29 strains were not strictly correlated with their vegetable sources, suggesting an influence from other factors, such as geographic origin and region-specific processing methods. Similar to the profiles of the 21 publicly available genomes, inactive prophages, intrinsic vancomycin resistance genes, and genomic island fragments were detected in eight isolates, whereas no known virulence genes were identified. Bacteriocin gene clusters varied among strains, while stress tolerance and probiotic-related genes were conserved. Overall, these results provide genomic indications relevant to the safety, adaptability, and fermentation potential of indigenous L. mesenteroides from Yunnan. However, because these functional traits are inferred solely from genomic predictions, subsequent experimental validation is essential to confirm their phenotypic properties and technological efficacy.