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Molecular cuisine for gut bacteria

EMBL scientists show how to grow a wide range of gut bacteria in the lab

European Molecular Biology Laboratory

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Credit: Aleksandra Krolik / EMBL

Scientific recipes to successfully grow and study gut bacteria in the lab: that's what EMBL* scientists are publishing in Nature Microbiology on March 19. They report on the nutritional preferences and growth characteristics of 96 diverse gut bacterial strains. Their results will help scientists worldwide advance our understanding of the gut microbiome.

The bacteria living in the gut have a big impact on our health. But researchers still don't know what kind of food most of our gut bacteria like to live on, or precisely how they metabolise nutrients. The current paper reports on the growth characteristics of the main human gut bacteria in nineteen different growth media with well-defined recipes. Peer Bork, Kiran Patil and Nassos Typas, all group leaders at EMBL Heidelberg, led the work.

"Our resource provides scientists with tools to experimentally investigate the gut microbiome ecology, going beyond correlations and identifying causes and effects," says Nassos Typas.

Surprise!

The research team selected 96 strains from 72 bacterial species, representing the most frequently occurring and most abundant species in the human gut plus important species linked to infectious or other types of gut diseases, like colorectal cancer and inflammatory bowel disease (IBD). While characterising their nutritional preferences and ability to produce various molecules, the researchers discovered unknown metabolic features of some bacteria.

"We were surprised to find new bacteria with the capability to utilize mucin, the protein that makes up mucus," says Kiran Patil. "These bacteria can contribute to inflammation and infection by weakening the protective mucus barrier lining the gut. Another surprise came from bacteria that proved to be inhibited by amino acids and short-chain fatty acids, common ingredients in most growth media. It turns out that rich media with many nutrients can be toxic for these species, whereas we used to think: the more food, the better."

Furthermore, even closely related bacteria sometimes had completely different nutritional preferences. This shows that microbiologists can't base their assumptions about metabolic capabilities on bacteria's genetic relationships alone.

The new scientific 'cookbook' is filled with molecular recipes on how to grow gut bacteria, providing the community with the tools for studying the structure and function of the human gut microbiome.

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The first authors of the paper are Sergej Andrejev and Melanie Tramontano, who work as a scientific programmer and a postdoctoral fellow in the Patil group at EMBL Heidelberg, respectively.

*EMBL is Europe's flagship laboratory for the life sciences. We are an intergovernmental organisation established in 1974 and are supported by over 20 member states.

EMBL performs fundamental research in molecular biology, studying the story of life. We offer services to the scientific community; train the next generation of scientists and strive to integrate the life sciences across Europe.

We are international, innovative and interdisciplinary. We are more than 1600 people, from over 80 countries, operating across six sites in Barcelona (Spain), Grenoble (France), Hamburg (Germany), Heidelberg (Germany), Hinxton (UK) and Rome (Italy). Our scientists work in independent groups and conduct research and offer services in all areas of molecular biology.

Our research drives the development of new technology and methods in the life sciences. We work to transfer this knowledge for the benefit of society.

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