Single‐cell rapid identification, in situ viability and vitality profiling, and genome‐based source‐tracking for probiotics products

Rapid expansion of the probiotics industry demands fast, sensitive, comprehensive, and low-cost strategies for quality assessment. Here, we introduce a culture-free, one-cell-resolution, phenome-genome-combined strategy called Single-Cell Identification, Viability Vitality tests, Source-tracking (SCIVVS). For each cell directly extracted from product, fingerprint region D2O-probed single-cell Raman spectrum (SCRS) enables species-level identification with 93% accuracy, based on reference SCRS database 21 statutory probiotic species, whereas C–D band accurately quantifies viability, metabolic vitality plus their intercellular heterogeneity. source-tracking, Raman-activated Cell Sorting Sequencing can proceed, producing indexed, precisely one-cell-based genome assemblies that reach ~99.40% genome-wide coverage. Finally, validated an integrated SCIVVS workflow automated acquisition where whole process except sequencing takes just 5 h. As it is >20-fold faster, >10-time cheaper, vitality-revealing, heterogeneity-resolving, automation-prone, new technological data framework assessment live-cell products.