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Microbes in the gut, lungs and biofilms do not simply exist as perfectly mixed populations; instead, they grow in layered and clustered three-dimensional (3D) arrangements. This spatial organization shapes how nutrients and chemical signals move between neighboring cells and how much oxygen different microbes can access. Scientists are increasingly recognizing that the relative spatial arrangement of microbes plays a role in digestion, immunity and overall health.
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Furthermore, the organization of microbes also influences their community behavior, interspecies interactions and physiology. In other words, to truly understand microbial communities, it is important to know not just which microbes are present but where each one is positioned.
The limits of current models
Recreating structured microbial communities in the laboratory, however, has proven difficult. Standard culture methods usually grow microbes in well-mixed liquid or on flat agar surfaces, making it hard to capture the 3D organization seen in living systems. More advanced methods can build 3D structures, but they typically rely on hydrogels or other solid materials to hold microbes in place.
While these methods can maintain a colony's shape, they can also limit bacterial movement, proliferation and molecular diffusion, thereby compromising the dynamic liquid environments found in natural microbial communities.
A liquid scaffold for microbes
To address this challenge, a research team led by Associate Professor Masayoshi Tanaka from the Department of Chemical Science and Engineering, Institute of Science Tokyo (Science Tokyo), Japan, in collaboration with Suntory Global Innovation Center Ltd., Japan, has developed the world's first liquid platform capable of engineering floating 3D microbial architectures, called "floatony."
This study, published in Biofabrication, describes a technique for creating and maintaining complex 3D microbial structures entirely within a liquid without solidifying the surrounding medium.
The team's approach uses a liquid containing microbes, or "bacterial ink," which is drawn into a "canvas solution" through careful 3D injection with a robotic arm. By carefully tuning the physical properties of the canvas solution, the researchers were able to keep the drawn microbial structures suspended in place without sinking, floating away or dispersing.
Through rheological measurements, the researchers established practical design principles for liquid environments that simultaneously maintain structural stability and molecular diffusion.
Keeping cells active in 3D
Using Escherichia coli as a model organism, the researchers demonstrated that bacteria in floatonies remained alive and metabolically active. In enzyme activity tests, the bacterial cells were able to process a substrate and release reaction products that diffused outward into the surrounding liquid.
"Unlike traditional hydrogel- or microfluidic-based methods, our approach maintains the intrinsic fluidity of the culture medium, allowing microbial motility, diffusion, and self-organization under minimally constrained conditions. This enables us to study and engineer microbial spatial organization under conditions that more closely resemble natural liquid environments," says Tanaka.
Potential for health and industry
Overall, the findings suggest that floatonies could become a useful experimental platform for studying how spatial organization affects microbial behavior. By bridging the gap between simple liquid cultures and rigid microfluidic or gel-based systems, floatonies offer a new window into how microbial communities take shape and how their spatial arrangement could be studied and engineered in the laboratory.
"In the future, the proposed platform could contribute to a better understanding of how microbial spatial organization influences health and disease, while enabling the rational design of microbial living materials," concludes Tanaka.
"We believe this platform could provide new opportunities for designing functional microbial communities for industrial biotechnology," adds Ippei Inoue of Suntory Global Innovation Center Ltd.
More information: Hidetaka Taniguchi et al, Floatony formation in liquid environments: liquid drawing-based fabrication of three-dimensional microbial structures, Biofabrication (2026). DOI: 10.1088/1758-5090/ae7ed4
Provided by Institute of Science Tokyo
This story was originally published on Phys.org.
