Transcriptomic and metabolomic analysis of Lactiplantibacillus plantarum growth phase Transition: Key pathways and metabolites

Abstract

The changes in the gene expression profiles and metabolite levels of Lactiplantibacillus plantarum (L. plantarum) are critical factors that influence its growth stages. Despite the significance of these factors, the specific genes and metabolites that influence growth stage transitions remain poorly understood with limited available data. To address this knowledge gap, we conducted transcriptomic and metabolome sequencing analyses using Illumina technology on six L. plantarum strains (MGA9-2, MGA9-3, KNY-16, KNY-17, R3-4 and SNR-9) during the logarithmic and stationary growth phases. Our analysis revealed 342 differentially expressed genes (FDR<0.05, | log (Fold Change) |>1) and 144 differentially expressed metabolites (VIP>1, p < 0.05). Compared to the logarithmic phase, the stationary phase exhibited 254 up-regulated and 88 down-regulated genes. KEGG pathway enrichment analysis and GO functional annotation revealed that 16 key differentially expressed genes were primarily linked to purine metabolism (p < 0.05). Additionally, the stationary growth phase displayed 39 up-regulated and 105 down-regulated metabolites. Additional screening using a threshold of | log2 (Fold Change) |>1 identified 4 up-regulated and 12 down-regulated key differentially expressed metabolites. The down-regulated metabolites, such as taurine, were linked to cysteine metabolism, which preserves the integrity of the cell membrane. By analyzing the interactions between these key differentially expressed genes and metabolites, we identified four key pathways, including d-amino acid metabolism, tryptophan metabolism, ABC transporters, and sulfur metabolism, involved in the transition of L. plantarum from the logarithmic to the stationary growth phase. These results provide theoretical basis for the industrial application of L. plantarum.