Finding microorganisms with macroporous silicone chips

From the gut to the seabed: microorganisms populate almost every habitat. The diversity of their survival strategies harbours great potential for biotechnology. However, the majority of these organisms are unknown because they cannot be cultivated. In order to better utilise this „microbial dark matter“, a research team from the Karlsruhe Institute of Technology (KIT) has now developed a „sponge“ made of porous, mouldable silicone. Embedded in a chip, microorganisms from the environment accumulate in the material, which are then available for further research. The results were published in ACS – Applied Material and Interfaces.

„It is astonishing that nobody has yet thought of using medical silicone for bacterial colonisation“, says Christof Niemeyer, Professor of Chemical Biology at the Institute of Biological Interfaces-1 at KIT. The advantages are obvious: the special polymer, which is also used for breast implants, for example, does not interact with its environment, is easy to modify, durable and inexpensive. According to the chemist, he and his team only came up with the idea in a roundabout way, but the results have exceeded their expectations. „The material is able to absorb the microorganisms from the environment, no matter how moist or dry it is. The prerequisite for this: the silicone had to be processed into a porous sponge-like structure," he explains.

Numerous different bacteria „caught“

In the course of several experiments, it became clear that the silicone sponge "captures" a particularly broad spectrum of microorganisms in its numerous holes. The team was able to identify members of the Actinobacteriota in the dry air of a chicken farm, for example. The exciting thing about this is that it is precisely these microorganisms that are used in the production of antibiotics. They can also produce substances that could help with certain types of cancer, for example. If we capture new bacteria with the sponge, they can be used for new impulses in biomedicine, for example," Niemeyer adds.

A similar thing happened after the silicone sponge was immersed in a breeding tank for zander. Compared to a conventional material that is already on the market, the researchers found, among other things, a large number of bacteria that belong to the still little researched Candidate Phyla Radiation.

These microorganisms make up around 70 percent of microbial dark matter, as they cannot yet be cultivated,

explains Professor Anne-Kristin Kaster, who analysed the captured microorganisms with her team at the Institute for Biological Interfaces-5 at KIT using state-of-the-art sequencing technology.

Silicone sponge produced with the help of table salt

The team also proved that selected bacteria can accumulate in the sponge if it is prepared accordingly. For example, micro-organisms that process glyphosate were „cuted“ into the sponge with this pesticide. The porous material was also colonised by microbes within a few days of contact with soil samples.

In order to make the medical silicone habitable for microorganisms, the researchers had to reprocess the material. The team mixed table salt into the polymer, which was then dissolved again. This created small holes connected by fine threads: the desired sponge-like structure. The researchers then moulded a „chip“ in order to be able to use it for the applications. This small unit is made of the same silicone as the sponge, but in its homogeneous, non-porous form.

„The practical thing is that the silicone chip – as a combination of sponge and chip – can be produced very easily using standard methods, in almost any size and number of pieces “, says Niemeyer. „In the end, you have a robust research tool that can be used in virtually any environment. Everything indicates that this chip is very well suited for the systematic investigation of microbial dark matter and also opens up interesting possibilities for the cultivation of previously uncultivable microorganisms.“

The macroporöse silicone chip has been filed for patent.

Source: LABO from 21 November 2022