Excessive post-acidification remains a major quality concern in yogurt production, yet the strain-specific mechanisms in Streptococcus thermophilus starter cultures are unclear. This study compared the post-acidification capacity of FS (strong) and FW (weak) strains through integrated physiological and molecular analyses to elucidate the dominant role of F_oF₁-ATPase–mediated proton homeostasis during storage. Although both strains exhibited similar acidification and lactose consumption during fermentation, FS accumulated more lactic acid during storage (6.89 vs. 6.49 g/L) and showed a smaller decrease in intracellular pH (ΔpHi 0.08 vs. 0.26), indicating superior proton homeostasis under acid–cold stress. Physiological assays revealed that FS showed higher F_oF₁-ATPase activity (1.17 μmol Pi/min/mg protein) and ATP levels (0.39 μmol/mg protein) at the storage endpoint. FS also maintained a membrane with a lower UFA/SFA ratio of 1.90, suggesting increased rigidity. Transcriptomics further showed that FS reinforced the F_oF₁-ATPase efflux pathway, aided by auxiliary neutralization and membrane-stress pathways. FS suppressed energy-costly biosynthesis and transport, forming a more integrated regulatory program than FW to sustain proton homeostasis. Notably, CcpA was upregulated in FS and was associated with this energy-conserving transcriptional profile, which may support proton transport and contribute to improved proton stability and reduced post-acidification under acid–cold stress. These findings provide mechanistic insights into strain-specific post-acidification and offer molecular targets for starter culture selection.

The addition of Bifidobacterium animalis subsp. lactis and prebiotics to fermented milk can enhance its flavor and sensory properties; however, research on the effects of their combined supplementation on flavor profiles remains limited. This study investigated the impact of simultaneously adding B. lactis IU100 and resistant starch type III (RS3) to fermented milk on flavor and texture. The results showed that co-supplementation shortened the fermentation time by 1 h. It also increased hardness by 28.8%, springiness by 1.14 mm, and water holding capacity by 12.45%, accompanied by the formation of a more continuous and dense gel network. Headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry (HS-SPME-GC-MS) combined with odor activity value analysis indicated the enrichment of 115 key aromatic compounds, among which ethyl caprylate, ethyl n-butyrate, 1-octanol, and 2,3-heptanedione were identified as representative flavor compounds associated with fruity and creamy notes. KEGG pathway analysis revealed that 24 differential metabolites were predominantly enriched in purine metabolism and amino acid-related pathways. Within these pathways, coordinated enzymatic reactions convert α-keto acids and fatty acid metabolites into key flavor esters and catalyze the formation of volatile alcohols from amino acids and aromatic fatty acid precursors. Overall, this combined strategy effectively optimized fermentation efficiency, texture, and flavor through the targeted reprogramming of microbial metabolic flux.