Genomic insights into dominant lactic acid bacteria in spoiled plant-based meat analogues

The rapid growth of the plant-based meat analogues (PBMAs) market has sparked interest in its nutritional and environmental benefits, yet the microbial safety and spoilage dynamics of these products remain poorly characterized. In this study we isolated 60 lactic acid bacteria (LAB) from soy- (SBM) and pea-based meat (PBM) products stored at 4 °C or 22 °C until spoilage and performed whole-genome sequencing to characterize their phylogeny, metabolic capacity, and secondary-metabolite profiles. Phylogenomic analysis revealed that Latilactobacillus curvatus and Latilactobacillus sakei dominated SBM, while Weissella viridescens and W. cibaria were prevalent in PBM. Functional annotations indicated heterofermentative metabolism and diverse glycoside hydrolase repertoires in Latilactobacillus , particularly GH1, GH13, and GH32, facilitating degradation of plant-derived carbohydrates in SBM such as trehalose, fructans, and polyphenol glycosides. In contrast, Weissella uniquely encoded complete pathways for menaquinone and tetrahydrofolate biosynthesis, which may enhance redox balance and nucleotide/amino acid synthesis under vitamin-limited storage conditions, supporting persistence in PBM. Across both storage conditions, temperature exerted minimal selective pressure on dominant LAB identity. The heterofermentative physiology common to these LAB supports spoilage in PBMAs. In addition, their dominance likely reflects high initial loads in raw ingredients and genomic capacity for inhibitory metabolites (e.g., class II bacteriocins and, in some lineages, 2-deoxy-streptamine-like aminocyclitol pathways). Building on prior amplicon surveys, this study provides species-level resolution and foundational functional-genomic insights into dominant PBMA spoilage taxa, revealing potential targets for control to extend shelf life and improve the microbial safety of PBMAs. • Plant-based meat analogues (PBMAs) spoilage dominated by lactic acid bacteria (LAB) • Latilactobacillus and Weissella are main LAB isolates. • LAB isolates show diverse carbohydrate and amino acid metabolism strategies. • Bacteriocin and aminoglycoside-like gene clusters found in LAB genomes. • All 60 isolates lacked virulence and functional AMR gene clusters.