As the probiotic industry evolves, the need for effective strain optimization is becoming increasingly important and there is a variety of technologies available to do this, including phenotypic and genetic selection, gene editing and transgenic techniques.
But Traitomic, a spin-off from the Carlsberg Group, has developed a new technology that aims to deliver solutions which fit with consumer and regulatory expectations across the globe.
Speaking at NutraIngredients’ IPA World Congress and Probiota conference in Dublin last week (Feb. 11-13), Toni Wendt, Traitomic’s co-founder and head of technology, explained the development of FIND-IT (Fast Identification of Nucleotide variants by droplet) technology followed 30 to 40 years of development and improvement of bacterial strains that are fundamental for brewing.
“Carlsberg has probably developed one of the keenest, fastest and most precise way of identifying specific genetic changes and specific genes in specific strains,” he told delegates.
The FIND-IT genetic screening tool stands out from other strain improvement technologies thanks to its ability to preserve the unique character of a strain, avoiding transgenic modification, Wendt explained. This makes it possible to identify optimised versions of a strain with new and desirable properties without impacting their already favourable characteristics and functionalities.
He argued the platform provides not only regulatory and consumer acceptance globally, but also the ability to identify genetic traits down to nucleotide level, and its speed allows users to compete within a fast-moving competitive landscapes.
The tech works by creating diverse libraries of genetic variants from one microbial strain which are pooled smartly and scanned using Droplet Digital PCR (ddPCR). This allows scientists to partition samples into thousands of nanoliter droplets, in order to screen for specific, predetermined DNA variations (nucleotide changes or knockouts).
Once a positive pool is identified, it is further analyzed in sub-pools until the specific, individual microbe carrying the desired trait is isolated.
Besides microbial strain optimization, the Carlsberg Research Laboratory has used the technology to screen vast libraries of genetic variants of barley in just two to three weeks, enabling the identification of plants with specific traits like improved flavor, higher yield and better resilience to heat and drought.
Traitomic officially spun out of the brewery’s research lab in January 2023 to bring this technology to other industries which want to optimize their crops or proprietary strains for improvements in yield, nutrition, flavor, or production.
Akkermansia optimization
Wendt presented a project his team undertook with researchers from the University of Copenhagen, in 2025. The researchers wanted to expand the genetic toolbox of Akkermansia muciniphila, by setting up a FIND-IT approach in this species to study the function of specific genes. As a starting point, genes putatively linked to antibiotic resistance were selected for the study.
The scientists had mapped many genes potentially involved in the production of anti-microbial compounds and needed to find a way to analyze these genes in detail.
“Traitomic has become very good at knowing how to set the perfect amount of genetic variation for the strain in question,” Wendt explained.
“We can put pressure on the DNA repair mechanism to the point where the strain cannot cope with that pressure anymore and makes mistakes, we can then measure at the how many nucleotide changes per genome that induces and can tailor that towards whatever number is required for a certain product application.”
Traitomic scientists screened for two specific nucleotide changes in the coding sequence of two putative proteins that may be part of efflux pumps —those involved in the pumping in and out of anti-microbial compounds.
“We can identify them in the library, we can purify them from the library, until we have a pure culture that has minimal collateral in the genome but has a specific genetic change in a specific amino acid that we have pre-selected to abolish the gene function of these pumps,” Wendt said.
The University researchers have taken the optimized strains to test and confirm whether they have found the genes involved in allowing anti-microbial strains in and out of the cell.
