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A new tool to capture ‘microbial dark matter’

| By Gerald Ondrey

Microorganisms populate nearly any habitat, no matter how hostile it is. Their great variety of survival strategies is of huge potential in biotechnology. However, most of these organisms are unknown, because they cannot be cultivated. To make better use of this “microbial dark matter” (MDM), a team of researchers from Karlsruhe Institute of Technology (KIT; Germany; has developed a “sponge” made of porous, formable silicone. Embedded in a chip, the material sucks up microorganisms in the surroundings, which can then be applied for further research.

microbial dark matter

“It is quite surprising that nobody ever thought of using medical silicone for the settlement of bacteria,” says Christof Niemeyer, professor for Chemical Biology at KIT’s Institute for Biological Interfaces-1. The special polymer — used for breast implants, for example — does not interact with its environment. It can be modified easily, is long-lived and inexpensive. “The material can take up microorganisms from the environment, no matter how moist or dry it is. For this purpose, the silicone had to be processed to a porous, sponge-like structure,” he explains. The porosity was introduced into the polymer by adding sodium chloride, which was then dissolved, resulting in the sponge-like material. Modified and unmodified silicone were then combined to form “chips” (photo), as described in a recent issue of Applied Materials & Interfaces.

Experiments revealed that this silicone sponge captures a very large range of microorganisms in its pores. In the dry air of a poultry farm, the team identified Actinobacteriota species. These microorganisms are needed for the production of antibiotics. Moreover, they can be applied to produce substances to treat certain cancer diseases. “With the sponge, we can catch new bacteria that might benefit biomedicine,” Niemeyer believes.

When the silicone sponge was immersed into a pool to cultivate pikeperch, researchers found many bacteria belonging to the Candidate Phyla Radiation group — far more than in conventional, commercially available material. “These microorganisms account for about 70% of the microbial dark matter, as they have not been cultivable so far,” says professor Anne-Kristin Kaster from the KIT Institute for Biological Interfaces-5. She and her team analyzed the captured microorganisms using the latest sequencing technology.

A patent application has been filed for the silicone chip.