Microbiome Assessment in Fermented Foods - Why this Matters?
Fermented foods are surging in popularity, but most routine checks still sample only a narrow set of organisms. In collaboration with Mėmelio Fermentuotas we are mapping the full microbiome of fermented grain-based beverages to improve quality, consistency, and safety.
Using high-throughput DNA sequencing, we track beneficial probiotic taxa, providing a data-driven foundation for smarter quality control and transparent product claims. A whole-microbiome view reveals producer-specific “fingerprints,” lot-to-lot drift, and early safety signals that can affect reliability and consumer trust. Our results help producers substantiate probiotic claims, guide raw-material screening, and align processes with evolving food standards.
How we do it?
We apply 16S rRNA (bacteria) and ITS2 (fungi) metabarcoding alongside shotgun metagenomics across manufacturers and production batches. Standardised lab workflows and robust statistics quantify community structure, detect rare taxa, and flag anomalies for targeted follow-up where needed. This systems-level approach complements culture-based QC to deliver an actionable microbial “dashboard” for decision-making.
Partnering with manufacturers pursuing science-based quality control of fermented products provides real production contexts and enables validation that scales from R&D pilots to routine monitoring. These collaborations yield clearer specifications for starter cultures, early warnings when communities drift outside control ranges, and practical guidance for procurement and labelling—ultimately supporting safer, more consistent, and more transparent production.
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