Sorting Bacterial Cocultures Using Microfluidic Droplets

Source: uFluidix, written by Pouriya Bayat; research by Ibraheem Alshareedah, Katelyn M. Green, Sang-Min Shin et al. (Los Alamos National Laboratory) (November 7, 2026). AI-generated summary by biochip.com, published November 8, 2026. Not independently reviewed.

Researchers at Los Alamos National Laboratory developed a microfluidic method that lets bacteria grow together in liquid droplets before converting those droplets into sortable hydrogel particles. The approach, called post-assay photogelation, uses ultraviolet light to solidify droplets only after incubation, helping avoid the growth constraints of culturing bacteria inside gels. The team then used a commercial flow cytometer to sort particles and recover the bacteria inside them. That combination could make it easier to find and study interactions among microbes.

Keeping Bacteria in Liquid Until Sorting

Bacteria often live in communities, where species can affect one another in ways that are hard to study in bulk. Droplet microfluidics addresses this by placing small groups of cells in separate water-based compartments surrounded by oil. But sorting droplets with interesting results can require specialized equipment.

The researchers’ method changes the droplets only after the bacteria have had time to grow together. The droplets contain light-reactive ingredients, which ultraviolet exposure turns into a solid hydrogel. The team could then move the particles from oil into water, sort them with a flow cytometer, and use an enzyme to break down the gel and release the bacteria.

Choosing a Gel That Supports Growth

The team generated droplets with custom-made microfluidic chips. One design used a cross-junction with a 20-micrometer nozzle, while a flow-focusing design was used in sorting experiments. The droplets measured about 30 to 40 micrometers across and were incubated at 37 degrees Celsius for about 18 hours before gelation.

Gel chemistry mattered. In tests with Escherichia coli Nissle 1917, bacteria grown in liquid droplets before gelation showed stronger, more evenly distributed fluorescence than bacteria gelled at the start. A peptide-based gel formulation inhibited growth, so the team switched to methacrylated dextran, which supported growth and could later be broken down with dextranase. About 60 seconds of ultraviolet exposure solidified the droplets.

Sorting and Recovering the Cells

In a test using red and green fluorescent beads, a commercial WOLF G2 cell sorter produced sorted populations that were about 99.9% pure for green particles and 99.7% pure for red particles. In a separate test, sorting raised the share of particles containing fluorescent E. coli Nissle from 59% in the starting mixture to 98% in the collected sample.

The full workflow recovered about 69% of culturable bacteria, with a reported variation of plus or minus 9 percentage points. That recovery measure included encapsulation, gelation, transfer into water, and enzymatic breakdown of the gel, showing that the particles did not permanently trap all of the cells.

Testing a Nasal Microbial Community

The researchers also cocultured fluorescent E. coli Nissle with a bacterial community grown from human nasal samples. After incubation, the fluorescent strain was the predominant detectable population in droplets containing it. The result suggests that the strain may have inhibited community members under the conditions tested, but does not establish how it would affect nasal microbes more broadly.

Why This Matters

By postponing gel formation until after coculture, the method links liquid-phase microbial growth to conventional particle sorting and bacterial recovery. This could help researchers screen many small microbial communities and retrieve selected cells for further study. Future work can test how well the workflow handles other bacterial species and community combinations.

Topics: Microfluidics · Infectious diseases

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