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The genetic material of bacteria predicts their food preferences

6 October 2023
By analyzing many different strains of marine bacteria, microbiologist Matti Gralka and his team discovered that bacteria can be classified by their preference for sugars or acids – extremely useful information that makes it easier to understand the metabolic processes in many environmental microbial communities.

Preference of the bacteria
Bacteria often grow in communities of many co-occurring species, such as in your gut, in soil, or in the ocean, and will then have to work together. So-called heterotrophic bacteria use organic carbon sources. A fundamental process in these communities is that bacteria absorb the nutrient medium they need, so-called substrates such as sugars and amino acids, from the environment. They then convert this into biomass or something else that they can excrete.

Patterns in substrate preference
The researchers were curious about which substrates different bacteria can use, with a focus on substrates that are used as a carbon source. The researchers also looked at whether they could identify patterns in the use of substrates by the bacteria, but also whether they could predict which substrates bacteria can use by looking at which genes the bacteria code for. By analyzing the growth of 182 different strains of marine bacteria on 135 different potential carbon sources, Gralka and his team discovered patterns in the substrate preferences of the bacteria. Put simply, they found that some bacteria prefer sugars such as glucose over acids, and others do the opposite, preferring acids over sugars. This preference is recorded in the genetic material of bacteria, which makes preferences predictable based on the genetic material of the bacteria.

Easier way of looking at bacterial communities
This new research provides a way to classify bacteria according to their substrate preference, which in turn makes it easier to understand the metabolic processes in many bacterial communities in the environment. It also provides insight into the evolution of these preferences of the bacteria. The results show how the evolution of the genetic material of bacteria is shaped by fundamental biochemical limitations that bacteria face. These constraints make it a winning strategy for bacteria to evolve differently in different environments and thereby specialize into sugar or acid specialists. “Because the preferences are fixed in the DNA of the bacteria, we can estimate the substrate conversion capabilities of bacterial species that we have not (yet) grown, but for which we need genetic information,” says Gralka.

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