Scientists have introduced a high-throughput technique that can rapidly screen entire microbial communities for useful traits, revealing unexpected candidates from insect-associated microbiomes. Credit: Shutterstock

A new microdroplet-based technique allows scientists to quickly pinpoint bacteria that can boost vitamin B2 levels in soy drinks.

Researchers at the DTU National Food Institute have developed a faster way to identify bacteria that can both support fermentation and boost vitamin B2 levels in soy drinks. In this study, they analyzed the microbiome (the complete bacterial community) from bumblebees by isolating individual microbes in microscopic droplets and testing their ability to produce the vitamin.

“Our research shows that it is possible to screen entire microbial communities directly and rapidly, and that promising bacteria can be identified from environmental samples without prior isolation and analysis of individual bacteria. This can make the development of new starter cultures faster and more targeted,” says Associate Professor Claus Heiner Bang-Berthelsen from the DTU National Food Institute.

The findings were published in the journal LWT – Food Science and Technology.

Researchers have discovered promising bacteria in bumblebees

Plant-based dairy alternatives often contain fewer vitamins and minerals than cow’s milk, with vitamin B2 (riboflavin) commonly lacking.

To address this, the team focused on finding bacteria that could grow in soy drinks while naturally producing vitamin B2 during fermentation. They turned to bumblebee gut bacteria as a source of candidates.

“Bumblebees live close to plants, and their guts contain many microorganisms that are already adapted to plant-based environments. That is why it was interesting for us to test whether we could find bacteria in bumblebees capable of producing vitamin B2 in soya drinks,” says Postdoc Hang Xiao from the DTU National Food Institute.

Tested the bacteria in microscopic droplets

To carry out the screening, the researchers adapted a technique known as droplet screening. Each bacterium from the bee gut was enclosed in a tiny droplet that acted as its own miniature culture chamber, allowing millions of cells to be tested within hours using a microfluidic system.

“Unlike conventional agar plate-based methods for microbial cultivation and screening, we encapsulated the bee gut bacteria in microscopic droplets so that each droplet contained only one bacterium and acted as an enclosed culture chamber. In this way, the individual bacterium could be analyzed at ultra-high speed by using our microfluidics screening platform, enabling us to screen millions of bacterial cells within just a few hours,” says Hang Xiao.

Because soy drinks are typically cloudy and interfere with measurements, the team created a transparent soy medium to improve accuracy.

“By making the soya liquid transparent, we were able to both screen the bacteria in an environment resembling their future application and, at the same time, obtain more stable droplets and more precise measurements,” says Claus Heiner Bang-Berthelsen.

The bacteria were exposed to roseoflavin, a compound similar to riboflavin that encourages the growth of strong vitamin B2 producers. The brightest glowing droplets, indicating the highest vitamin production, were then selected.

“This droplet-based microbial screening approach saved months of work and significantly reduced the resource use compared with conventional screening methods,” says Claus Heiner Bang-Berthelsen.

A particular Lactococcus lactis strain stood out

Among the microbes identified, a strain of Lactococcus lactis stood out. When tested in real products, it performed especially well in soy drinks.

“The results suggest that the bacterium works not only under laboratory conditions, but also in actual foods containing a significant amount of protein,” says Hang Xiao.

The strain continued producing vitamin B2 even when the drinks were already fortified with high levels of the vitamin, showing stable performance. It also demonstrated the ability to use a wide range of sugars, making it a flexible option for fermentation.

However, the bacterium was less effective in rice, oat, and some almond drinks, likely due to their lower protein content. The researchers believe a sufficient level of fermentable protein is needed for optimal growth and vitamin production.

“The exciting thing about the method is that it can not only identify vitamin B2-producing bacteria in soy drinks. It can also be adapted to identify other interesting substances, provided they can be detected using fluorescence. However, the method only works if the medium is transparent and has a low fluorescence background,” says Hang Xiao.

Reference: “Droplet microfluidics-based isolation, adaptation, and screening of riboflavin-producing lactic acid bacteria for fermenting plant-based dairy alternatives” by Hang Xiao, Anders Peter Wätjen, Guillermo-Eduardo Sedó Molina, Egon Bech Hansen, Miguel Tovar and Claus Heiner Bang-Berthelsen, 14 January 2026, LWT.

DOI: 10.1016/j.lwt.2026.119036

The research was supported by, among others, Novonesis and the Innomission research project REPLANTED. Additional support was provided by DTU and FoodHay

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