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Foto: Marc Kolle

“Antibiotics destroy all bacteria, while only one bacterium is often the culprit”

Sija van den Beukel,
8 september 2023 - 10:38

The microbiome of Westerners is becoming increasingly unbalanced. Thus we need to change course, thinks Professor Marten Smidt, one of the founders of the National Holomicrobiome Initiative. With €200 million earmarked from the National Growth Fund, the project can now get started.

“This is what we’ve been doing all these years,” says professor of molecular neuroscience Marten Smidt, holding his hands before his eyes: “Lalalalala.” We use plenty of antibiotics and pesticides that kill bacteria and other microorganisms, the professor explains, despite the fact that we still do not sufficiently understand exactly what those microorganisms do in humans, plants, and the soil.

Foto: UvA
Marten Smidt will spend the next few years researching all microbiomes together

Meanwhile, the consequences are becoming increasingly clear: the soil is becoming impoverished, groundwater is becoming polluted and the number of intestinal diseases and obesity has risen sharply in recent years.


That’s why we need to change course, Smidt says. More knowledge is needed about the microbiome: the community of billions of microorganisms working together, such as bacteria, fungi, and viruses that are everywhere: in the soil, in water, in plants, in your intestines, and so on.


Isolated systems

In recent years, research often remained focused on one isolated system such as the gut microbiome. But according to Smidt, there needs to be overarching research for all microbiomes. “You can’t actually isolate microbiomes, you have to see them as a whole. Animals produce manure, manure ends up on the land, and plants grow there that animals eat again. So everything is interconnected.”


For that project - the holomicrobiome - the National Growth Fund recently earmarked €200 million. Over the next 10 years, the UvA, together with 10 Dutch universities, six medical research institutes, and numerous other research institutions and companies will conduct research on all microbiomes together.

“Most people grow up with the idea that you just have to kill a bacterium. Trust me - you really don’t want that”

The researchers are working on a huge mathematical model to understand how bacteria, fungi, and viruses work together. Says Smidt: “Previously, we mainly looked at what bacteria are present in a microbiome, but it is much more interesting to know what the bacteria do. After all, we ultimately want to know how a microbiome functions. We need to start figuring that out.”


Cow intestines

Many problems can be solved with that knowledge, Smidt says. Knowledge of how the microbiome works in cow intestines can provide insight into nutrition that can reduce methane and nitrogen emissions.



Alternatives to antibiotics can also be used. ““Antibiotics destroy all bacteria, while only one bacterium is often the culprit” Bacteriophages could be used as an alternative, Smidt suggests. Bacteriophages are viruses that can specifically kill one bacterium. “Companies in America already produce bacteriophages; the same should happen in the Netherlands.” Bacteriophages could also be used in agriculture instead of pesticides to combat specific pathogens.


A different way of thinking

Thus, the entire chemical approach to agriculture must eventually move to a natural one. And that requires a different way of thinking. “Most people grow up with the idea that you just have to kill a bacterium. Trust me - you really don’t want that.”

“What we call a pathogen is actually a bacterium that prevails because it doesn’t have enough competition”

“In any case, the word ‘pathogen’ is strange,” Smidt continues. “What we call a pathogen is in fact a bacterium that predominates because it doesn’t have enough competition from other types of bacteria. You could also just add more bacteria to rebalance the microbiome.”


Smidt could go on and on like this. “No, the microbiome is not the holy grail for everything, but it is important for people to be aware of the fact that we are part of a greater whole in which microbes are essential. We still need to do some work on that.”


That also means eating more unprocessed foods such as fruits, leafy vegetables, and fermented foods like yogurt and cottage cheese. “After all, they are crammed with bacteria,” Smidt says. And those are needed to keep the microbiome diverse and balanced to prevent intestinal disease. “Every person has about 1.5 kilograms of bacteria in their intestines that are needed to digest food. You are not born with that; you have to be exposed to it.”