Exploring hidden members in microbial communities

Dr. Christoph Ratzke from the University of Tübingen’s Interfaculty Institute for Microbiology and Infection Medicine is a researcher who likes to take his research off the beaten track. So his latest project to better characterize microbial communities from environmental samples fits in well with the Volkswagen Foundation's "Pioneering Research - Exploring the Unknown Unknown" program, through which he received almost 570,000 euros in funding for a period of three years in December 2023. The double "unknown" of the program is reflected in his project "The unknown majority - what is the role of 'unculturable' microbes in microbial communities?".

"Microbes are everywhere. Even a spoonful of soil contains thousands of different species. However, we can only cultivate and study one to ten percent of them in the laboratory," says Christoph Ratzke. He his aim is to get a more comprehensive picture of the entire microbial community. He is particularly interested in examining samples from bodies of both salt and fresh water, where scientists suspect there are many undiscovered bacterial species.

The majority of microbes in a community are barely recognizable in the laboratory; this has been a problem for some time, says Ratzke. Until now, however, there has been a lack of ideas on how to study them more closely. Ratzke is taking a new approach by not isolating the microbes. "It is very likely that many of the microbes that do not grow in isolation in the laboratory need a partner," he says. Therefore, he will seek to develop a culture system, for example, in which different microbial species are physically separated from each other, but the neighbors remain accessible for the exchange of substances,. The funding will allow him to hire a postdoc and purchase a large-scale device for the automated sorting of microbes.

Scientists in the laboratory have often been able to identify which microbes are most successful under competitive conditions. "However, I am interested in the entire biodiversity of natural microbial communities and the conditions under which they remain stable," says Ratzke. He aims to develop a method which will be applicable to microbial communities from all types of ecosystems. "Bacteria and fungi make use of many different metabolic pathways and produce a wide variety of substances that can be useful to humans, for example as antibiotics," he says. "There is enormous potential in these previously unexplored species."

The Volkswagen Foundation’s "Pioneering Research - Exploring the Unknown Unknown” funding initiative, supports groundbreaking and risky research ideas with high scientific relevance. It is for projects with the potential to achieve major scientific breakthroughs, even if there is a risk of failure. Ratzke is confident: "I don't see my research as risky in that sense. I see it more as open-ended.“

Text: Janna Eberhardt/Hochschulkommunikation