Comparative genomics and metabolomic profiling of Lactiplantibacillus plantarum LP104 reveal its potential in co-fermented yogurt.

Exploratory comparison of extracellular proteomic, metabolomic, and lipidomic profiling of inulin-fortified gelatin capsule waste gel fermented by Lactiplantibacillus plantarum

This exploratory study evaluated whether partial replacement of sucrose with inulin was associated with differences in the proteomic, metabolomic, and lipidomic profiles of gelatin capsule waste gel fermented by Lactiplantibacillus plantarum. A sucrose-based Control and an INU-50 formulation, in which 50% of sucrose was replaced with inulin, were compared using parallel proteomic, untargeted metabolomic, and untargeted lipidomic profiling. The Control and INU-50 groups separated clearly across all datasets. Proteomic analysis identified four proteins with higher abundance in the INU-50 formulation, including proteins putatively associated with carbohydrate transport, pentose phosphate metabolism, purine biosynthesis, and translation-related functions. Untargeted metabolomics detected 1885 molecular features, among which 426 differential features with putative metabolite annotations were identified in the original exploratory analysis. These features were mainly linked to carbohydrate metabolism, sugar interconversion, amino sugar and nucleotide sugar metabolism, cofactor metabolism, and intermediary carbon pathways. Untargeted lipidomics detected 6005 lipid-related molecular features, including 563 differential features with putative annotations, associated with fatty acid metabolism, glycerophospholipid-related compounds, cardiolipin-related species, ceramide-associated molecules, and secondary metabolite-linked lipid features. Integrated analysis indicated that the observed protein abundance patterns and extracellular molecular features were associated with differences between the two fermented formulations. These findings provide an exploratory molecular dataset describing associations between inulin fortification and complementary omics profiles during gelatin capsule waste fermentation. Because non-fermented controls and targeted validation were not included, mechanistic interpretation should be considered cautiously.

Integrated ¹H-NMR Metabolomics and Growth Kinetics Uncover Three Distinct Metabolic Scenarios in Lactiplantibacillus pentosus P7 Fermentation of Plant-Derived Prebiotics.

Metabolic engineering of Lacticaseibacillus paracasei alleviates post-acidification and reshapes metabolite profiles in probiotic yogurt

Post-acidification during storage limits the use of multiple probiotics in fermented dairy products. In this study, the ldh gene was deleted in Lacticaseibacillus paracasei Zhang (LCZ), resulting in 45% reduction in lactic acid production. Co-fermentation of the engineered strain with commercial starters effectively controlled post-acidification, maintained a stable pH (4.5–4.3) over 28 d, and increased production of volatile compounds (acetoin, decanoic acid, and dodecanoic acid) and bioactive metabolites (acetic and succinic acids). Metabolic analysis revealed that ldh deletion activated acetoin biosynthesis (750 ng/mL) and redirected carbon flux toward malic, and acetic acids. The modification also promoted amino acid catabolism (L-alanine, L-cysteine, and L-asparagine) to pyruvic acid, enabling nitrogen–carbon co-utilization. This study presents a promising solution for developing stable probiotic dairy products and provides new insights into probiotic metabolic engineering.

Integrating Metabolomics and Transcriptomics Reveals the Multi-Target Mechanisms of Fermented Portulaca oleracea L. (Purslane) in Attenuating Acute Diarrhea

Background: Current understanding of the biotransformation of bioactive compounds in Portulaca oleracea through probiotic fermentation remains limited, and the anti-diarrheal mechanisms of the resulting fermented products have yet to be fully elucidated. Methods: In this exploratory study, we employed untargeted metabolomics together with a senna-induced acute diarrhea mouse model to investigate P. oleracea co-fermented with Lactiplantibacillus plantarum and Bacillus subtilis. Results: Metabolomic profiling identified 220 metabolites significantly altered by fermentation, predominantly comprising increased levels of lipids, phenylpropanoids, and polyketides. Compared with the unfermented P. oleracea control, fermented P. oleracea (FP) effectively reduced the diarrhea index, lowered serum levels of inflammatory cytokines (IL-1β, IL-6, TNF-α) and neurotransmitters (5-HT, substance P), and restored Na+/K+ balance as well as ileal histomorphology. Transcriptomic analysis and RT-qPCR validation further demonstrated that FP modulated the expression of genes involved in focal adhesion, PI3K-Akt, cGMP-PKG, and mineral absorption pathways. Conclusions: Fermented P. oleracea (FP) alleviates acute diarrhea through multi-target mechanisms. Notably, fermentation endows P. oleracea with markedly superior intestinal protective effects relative to the unfermented counterpart. These findings provide preliminary experimental evidence supporting the potential of fermented P. oleracea as a candidate for intestinal protective functional food research.

Starter-Culture-Dependent Effects of Lactiplantibacillus plantarum and Lactobacillus delbrueckii subsp. bulgaricus Fermentation on Nutritional Quality, Flavor Characteristics and Metabolite Profiles of Flammulina velutipes Roots

Flammulina velutipes roots, abundant edible mushroom by-products, have potential for value-added utilization. This study evaluated the effects of Lactiplantibacillus plantarum (Lpb. plantarum) and Lactobacillus delbrueckii subsp. bulgaricus (Lab. bulgaricus) fermentation on the physicochemical properties, antioxidant activity, flavor characteristics, sensory characteristics, and metabolite profiles of F. velutipes roots. Fermentation significantly increased soluble dietary fiber (SDF) from 1.537 to 1.722 g/100 g and DPPH radical scavenging activity from 27.88% to 59.92% in Lpb. plantarum-treated samples. GC-IMS analysis showed that fermentation increased several flavor-active aldehydes, esters, alcohols, organic acids, and ketones, thereby improving aroma complexity. LC-MS-based untargeted metabolomics revealed that amino acid metabolism, fatty acid metabolism, organic acid metabolism, and phenylpropanoid-related pathways were closely associated with flavor formation and antioxidant enhancement. Both Lpb. Plantarum and Lab. bulgaricus fermentation enhanced the accumulation of organic acids, sugar alcohols, and aromatic precursors, supporting improved antioxidant activity. Notably, Lpb. plantarum elicited broader metabolic shifts involving hydroxy fatty acids, esters, while Lab. bulgaricus more strongly promoted organic acid and aromatic metabolite accumulation, contributing to a more acidic and malty flavor profile. Sensory evaluation and electronic tongue analysis further confirmed that fermentation enhanced aroma and palatability, while increasing sourness and reducing bitterness and astringency. These results suggest that starter-culture-dependent lactic acid bacteria fermentation is an effective strategy for improving the functional and sensory characteristics of F. velutipes root by-products.

Multi-omics reveals metabolic division of labor in mixed-starter soymilk fermentation.

Fermentation by multiple microorganisms significantly improves the sensory quality and nutritional value of soymilk, yet the molecular mechanisms underlying the synergistic interactions, particularly regarding substrate utilization and nutrient exchange were not clear. Here, metatranscriptomics and non-targeted metabolomics were integrated to characterize the microbial succession and metabolic reprogramming of a mixed starter culture (Streptococcus salivarius subsp. thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, and Lactiplantibacillus plantarum) during soymilk fermentation. Taxonomic analysis revealed a cooperative succession pattern, where S. thermophilus dominated the mid-stage fermentation, facilitating the subsequent dominance of L. plantarum in the late-stage. Controlled soymilk fermentation with systematic exclusion of single strains, omics results elucidated a sophisticated metabolic division of labor. Specifically, S. thermophilus acts as the primary oligosaccharide metabolizer, as its absence induced compensatory galactose utilization pathways in the remaining strains. Furthermore, the removal of L. bulgaricus led to the significant derepression of vitamin and amino acid biosynthetic gene clusters, providing transcriptional evidence that L. bulgaricus functions as a key cross-feeding bacterium to support the auxotrophic community via cross-feeding. These findings unravel the essential gene-metabolite linkages driving synergistic fermentation and offer a theoretical basis to robustly reproduce fine fermented soymilk characteristics.