Nothing so resilient as a microbiome

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BY Hanny Roskamp

November 2018

What doesn’t kill them makes them stronger, you could say of bacteria. Which is why they are used to clean up numerous harmful substances, when decontaminating soil, for instance. Yet there are also attacks which micro-organisms cannot cope with. “That’s why you should always have a few in reserve.”

Animals, humans and the soil they walk on have something in common. They all host a lively ‘zoo’ of bacteria and other microscopic organisms. In humans and animals, most of the microbiome is found in the bowels (as well as on the skin and in the nose and mouth). In the soil – and other places such as groundwater and surface water – the bacteria are spread throughout the space. Hauke Smidt researches the resilience of these populations when they are under attack, perhaps from soil pollution or antibiotics.

Researchers are looking at what wild boar and raised pigs eat, and how that affects their microbiome. PHOTO Hollandse Hoogte

One thing is clear: a microbiome (a community of different bacteria) is naturally resilient. Smidt: “Most bacteria grow at great speed and in large numbers, which enables them to adapt quickly to changing conditions. If bacteria are repeatedly exposed to harmful substances, for example, their capacity to withstand them goes up. That is a characteristic which is more and more often used in decontaminating groundwater and surface water or polluted soils. And even in an environment that is full of plastics, bacteria have been found that can actually break down certain plastics – something which for a long time we thought was impossible.”

Resilience affected by antibiotics

But the resilience of the microbiome does buckle in the face of certain disturbances, which do permanent damage. One example is the long-term, large-scale use of antibiotics, as was still normal in livestock farming 10 years ago, and even the incidental antibiotic use that still takes place.

‘Poo transplants are being used to try to restore the resilience of a badly disturbed microbiome’

Smidt is currently studying the impact of such disturbances on farm animals. “On the animal’s health in particular. That is why we don’t just look at the impact of antibiotics on the microbiome of farm animals, but we are also now comparing what wild boar and raised pigs eat, and how that affects their microbiome. And we study how we can apply that knowledge in livestock farming. That is important for human health as well: after all, humans, animals and the environment make up one ecosystem. Increasingly, this is the basis of the One Health approach.”

A fit microbiome requires functional diversity: the presence of bacteria that can carry out a range of different tasks. PHOTO Hollandse Hoogte

The resilience of the microbiome is essential to human health as well. “The poo transplants that are being carried out by doctors are a case in point. The aim there is to restore the resilience of a badly disturbed microbiome. Another of the possibilities is to develop special pre-, pro- and synbiotics which are crucial to
a healthy microbiome.”

In poo transplants the aim is to restore the resilience of a badly disturbed microbiome. ILLUSTRATION Vector Mine/Shutterstock


Prof. Hauke Smidt


Personal professor of Microbial Ecology at Wageningen University & Research

Resilience research

The resilience of microbial ecosystems


Hauke Smidt works on this research with a team of scientists from Wageningen University & Research, TU Delft and the Netherlands Centre for One Health

At this point we have a reasonably good overview of the characteristics of a fit and resilient microbiome. Smidt: “The most important feature is functional diversity, the presence of bacteria that can carry out a range of different tasks. And then several species of all the types, including both generalists and specialists. It is important that if one of them gives up the ghost, another can take over from it, a kind of reserve pool, so you want a microbiome that is as biodiverse as possible. Of course there are resilient species and less resilient species. And there are dominant species, which are present in large numbers. And yet the rarer species are needed for a healthy, resilient community.”

‘The communication between micro-organisms contributes to their response capacity’

Communication between microorganisms contributes to their ‘response capacity’ too. “They communicate by secreting hormone-like substances (pheromones) as well as through the products of their metabolism (metabolites).”

Knowledge about the resilience of microbiomes is not just important for the health of plants, animals and humans, but can also be used in biotechnology. Here, drugs and other substances are produced by specialist bacteria that are ‘trained’ or bred for that task. Usually just one bacterial species is involved, a monoculture. Smidt: “It has turned out that those monocultures are vulnerable, so in biotechnology people are shifting more towards mixed cultures, which are more resilient and less vulnerable.”

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