Nutrients from the environment can disrupt the microbiome and lead to disease development

CRC 1182 study shows that environmental nutrient composition directly influences the microbial colonisation and pathogenesis of the freshwater polyp Hydra.

Since the midd-20th century, there has been an increase in so-called modern diseases, in parallel with a progressive decline in the diversity of the human gut microbiota, linked to changes in lifestyle and diet in industrialised societies. Researchers believe that these modern diseases, such as chronic inflammatory bowel disease, are caused by perturbations in the human microbiome. How changes in the body’s microbiota are linked to the mechanisms of disease development is currently the subject of debate in the scientific community. A team from the Collaborative Research Centre (CRC) 1182 “Origin and Function of Metaorganisms” at Kiel University, Germany, has proposed that certain bacterial species within the microbiome can switch from a neutral to a harmful effect on the host organism depending on the nutrient supply of the environment – and that the environmental conditions could therefore provide a decisive impulse for the composition of the microbiome and its involvement in the development of disease.

Using the freshwater polyp Hydra as an example, the researchers were able to show experimentally that differences in the natural nutrient supply of the surrounding water lead to significantly different microbiome compositions in the animals. Using a combination of different colonising bacterial species and the addition of different nutrients, they also showed that the presence of certain bacteria only leads to the development of disease when a specific nutrient is added. This indicates that the supply and composition of nutrients in an organism’s environment can influence its microbiome, causing dysbiosis and subsequently disease. In a recent publication in the American Society for Microbiology’s scientific journal mBio, the Kiel researchers thus provide an extended ecological explanation for the development of environmental diseases, which they previously published as a hypothesis, also in mBio (Lachnit et al. 2019).

Analysing the microbial composition under natural environmental conditions
The Hydra microbiome has been well studied under laboratory conditions, with numerous studies demonstrating the involvement of the microbial community in several key life processes. “The establishment of this functionally essential microbiome is usually explained by the coevolution of a host organism and specific microbes that have adapted to each other in such a way that, over time, a relatively stable, host-controlled microbial colonisation develops that provides the host with the functions it needs,” says Dr Tim Lachnit, a researcher in the Cell and Developmental Biology group at the Zoological Institute.

However, little attention has been paid to how natural environmental conditions can affect the polyps’ microbiome. The scientists therefore investigated whether their microbial communities changed when the animals were exposed to natural lake water with different nutrient levels. “We introduced animals with a typical laboratory microbiome into six lakes in Schleswig-Holstein with different nutrient levels. After seven days in the natural environment, we analysed the composition of their microbial communities,” continues CRC 1182 member Lachnit.

When the researchers repeated their experiments with different nutrient concentrations under laboratory conditions, they found that the composition of the polyps’ microbiome had changed significantly: Compared to the laboratory microbiome, several previously unrepresented bacterial species were added and the abundance of species also shifted significantly. “If there is a stable microbiome controlled by the host, such a global change should not occur. Therefore, our observations point to altered nutrient conditions in the surrounding water as the decisive influencing factor,” the Kiel biologist emphasises. They were also able to show that the environment influences the microbial community of the host through microbial transport. “The complexity of the interactions between communities, in this case between the microbiome of the host and the microbial community in the water, is still poorly understood, but is of great importance in order to better predict the results of manipulations of the microbiome, such as the transplantation of faecal microbiota,” says Dr Peter Deines, interim professor in the Evolutionary Ecology and Genetics group at the Zoological Institute.

How does changing the nutrient supply affect the microbiome?
To investigate the effects on the microbiome, the researchers artificially enriched the polyps’ environmental water with nutrients in the laboratory and then analysed the species composition again. “When we overfed the bacteria to a certain extent by adding a so-called complex nutrient mixture, the composition of the microbial community changed significantly. In addition, the phenotype of the polyps clearly showed signs of disease, such as shrinking tentacles. This allowed us to experimentally confirm our theory that overfeeding the microbiome makes you sick,” says Lachnit.

Under natural conditions, such as those found in a nutrient-rich lake, similar results were found: At a lower nutrient concentration than in the laboratory experiment, but still high for natural lake water, the disease phenotypes in the polyps persisted, although less pronounced. In addition, their population growth was greatly reduced. “In general, we can conclude that a high nutrient supply to the colonising bacteria causes damage to the host organisms, both individually and on a population level,” concludes Deines.

To attribute the harmful effects observed in the artificial complex nutrient environment to a specific cause, the researchers next tested how selected nutrients individually affected microbial colonisation. “We exposed the polyps to many different substances for 48 hours. In some cases, there was extreme variation in the species composition of their microbiome, with Pseudomonas bacteria, for example, reaching an abundance of 80 to 90 per cent,” says Deines. It was known from previous experiments that in Hydra, increased abundance of this genus is often associated with the development of disease and is also correlated with inhibited population growth. “So we already had evidence that Pseudomonas can negatively affect Hydra. However, the detrimental effects did not occur universally, but only in the presence of the nutrient,” explains Lachnit.

Changing environmental conditions can turn harmless bacteria harmful
To clarify this link, the researchers looked at the nutrient L-arginine, a simple amino acid. This substance is pH-neutral and is not toxic to Hydra itself, meaning that it cannot directly cause the pathogenic effect. “In a further experiment, we first sterilised Hydra and then recolonised it exclusively with Pseudomonas bacteria. While the addition of L-arginine had no effect on the germ-free polyps, all the animals colonised with Pseudomonas died in the presence of the nutrient,’ says Lachnit.

To understand this mechanism at a molecular level, the research team carried out a transcriptional analysis of both the polyps and the bacteria. “In the presence of L-arginine, many immune response genes are upregulated in Hydra, so the polyps try to defend themselves against the effects of the nutrient, for example by apoptosis. Ultimately, however, this is unsuccessful and the polyps shrink and die,” says Lachnit. In the Pseudomonas bacteria, it was found that genes are activated that indicate a lack of nutrients or the search for certain substances. “L-arginine provides the bacteria with substances such as phosphate and carbon. However, they also lack iron, which they then try to obtain from the host organism. This bacterial process damages the polyp cells and the search for the missing element triggered by the addition of L-arginine, leads to the development of disease and the death of the host organism,” explains Lachnit. These observations thus confirm that changes in environmental conditions, in this case caused by a single amino acid, can make an initially neutrally associated microbe potentially harmful and thus dangerous to its hosts, blurring the line between pathogenic and non-pathogenic microbes.

In summary, the new study shows a clear link between the host microbiome and environmental conditions: “Our results challenge the idea that host-associated microbial colonisation is primarily controlled by the host and that the causes of disease development are mainly found there. Instead, we have shown that the Hydra microbiome is also characterised by a dynamic interplay between the microbes present in the environment and the nutrient conditions of the surrounding water,” emphasises Lachnit. In the future, the researchers plan to investigate whether these findings can be transferred to other host organisms, including humans. ”If the correlations between nutrient availability and disease development hold true for humans, this could lead to interesting conclusions about human nutrition. This would open up completely new perspectives for a better understanding and possible therapeutic approaches for microbiome-associated environmental diseases in the future,” concludes Deines.

Original publications:
Tim Lachnit, Laura Ulrich, Fiete M. Willmer, Tim Hasenbein, Leon X. Steiner, Maria Wolters, Eva M. Herbst, Peter Deines (2025): Nutrition-induced changes in the microbiota can cause dysbiosis and disease development. mBio First published: 25 February 2025
DOI: 10.1128/mbio.03843-24

Lachnit T, Bosch TCG, Deines P (2019): Exposure of the host-associated microbiome to nutrient-rich conditions may lead to dysbiosis and disease development – an evolutionary perspective. mBio 10:e00355-19.
DOI: 10.1128/mBio.00355-19

This work was made possible by the collaboration of two doctoral students of the CRC 1182, several bachelor students, a technical assistant and the provision of the laboratories of Professor Thomas Bosch.

Images are available for download:
www.uni-kiel.de/de/pressemitteilungen/2025/056-lachnit-mbio-authors.jpg
Caption: Dr Tim Lachnit and Dr Peter Deines investigated how certain bacterial species within the microbiome can switch from a neutral to a harmful effect on the host organism depending on the nutrient supply in the environment.
© Dr Tim Lachnit

www.uni-kiel.de/de/pressemitteilungen/2025/056-lachnit-mbio-disease.jpg
Caption: Overfeeding with high nutrient availability changed the composition of the polyps’ microbiome and led to clear signs of disease, such as the shrinking of their tentacles.
© Dr Tim Lachnit

www.uni-kiel.de/de/pressemitteilungen/2025/056-lachnit-mbio-tl.jpg
Caption: Together with colleagues, Lachnit was able to prove that the nutrient supply and composition of a living organism’s environment can influence its microbiome in such a way that dysbiosis and, as a result, diseases develop.
© Dr Tim Lachnit

www.uni-kiel.de/de/pressemitteilungen/2025/056-lachnit-mbio-samples.jpg
Caption: The researchers were able to show experimentally that differences in the natural nutrient supply of the surrounding water lead to significantly different microbiome compositions in the hydras.
© Dr Tim Lachnit

Contact:
Dr Tim Lachnit
Cell and Developmental Biology
Zoological Institute, Kiel University
Phone: +49 431-880-4171
Email: tlachnit@zoologie.uni-kiel.de

Dr Peter Deines
Evolutionary Ecology and Genetics
Zoological Institute, Kiel University
Phone: +49 431-880-4140
Email: pdeines@zoologie.uni-kiel.de