Teaching old dogs new tricks: Extending existing theory on host-microbiome evolution

CRC 1182 research team proposes further development of existing evolutionary theory to better understand the interconnected evolution of host organisms and microorganisms

The microbiome comprises a multitude of bacteria, viruses and fungi that exist in and on a multicellular organism. The interactions of body cells and the microbiome form a structural and often functional unit, the so-called metaorganism. These interactions significantly influence the biology of both the host and the associated microbes. The Collaborative Research Centre (CRC) 1182 “Origin and Function of Metaorganisms” at Kiel University has been investigating these interactions in detail over the last decade. One aspect that has received little attention so far is how these interactions really shape the evolution of hosts and their associated microorganisms

To rectify this knowledge gap, researchers of the CRC 1182 at Kiel University, including Dr Bob Week and Professor Hinrich Schulenburg, who is also spokesperson of the CRC 1182, joined forces with international colleagues, such as Professor Brendan Bohannan from the University of Oregon and additionally Mercator fellow of the CRC 1182. Based on a critical survey of existing theory, this international group of scientists are proposing several novel theoretical approaches and conceptual frameworks to stimulate and guide new research on how host-microbiome interactions shape the process and dynamics of evolution. These novel concepts are published today in the renowned scientific journal Nature Ecology and Evolution.

Microbiomes form a significant factor in heredity
The study of host-microbe interactions and their involvement in central life processes is at the core of current research in the life sciences. Researchers have shown in a wide range of studies that host-associated microbiomes can influence many key functions of their hosts and thereby affect the organisms’ evolutionary fitness. Indeed, several studies strongly suggest that the microbiome decisively supports the host’s ability to adapt to new environmental conditions and thereby shapes host evolution. This far-reaching influence is surprising, because host-associated microbes are not necessarily transmitted from parents to offspring, while some kind of inheritance from one generation to the next is required for evolution to occur. This then raises the question of how traits mediated by the microbiome are really passed on from generation to generation.

Theoretical models show high potential to disentangle such complex relationships, identify key contributing factors, and thereby generate hypotheses for new research. In spite of the particular current interest in metaorganism research, dedicated theoretical frameworks on host-microbiome evolution are surprisingly scarce. “Currently most biologists consider the evolutionary influence of the microbiome as a kind of extended inheritance phenomenon, for which there are already various theoretical frameworks available in evolutionary biology,” emphasised Bohannan, who is staying at Kiel University over the summer in his role as a Mercator Fellow of the CRC 1182. “However, most evolutionary theory was not developed with microbiomes in mind, and I don’t think current theory is sufficient to provide a comprehensive understanding of the impact of microbiomes on metaorganism evolution. The goal of our new work is to take the first steps toward developing evolutionary theory that has host-microbiome biology at its core,” continued Bohannan.”

Expanding existing evolutionary concepts
The international team of authors, additionally including Professor Shelbi Russell from the University of California, Santa Cruz, and Professor Marjolein Bruijning from the University of Amsterdam, therefore scrutinized the most frequently discussed theoretical concepts to explore their application for describing microbiome-mediated evolution. One example is a phenomenon termed niche construction. “Niche construction is comparable to farming, where a farmer grows crops and livestock to ensure the availability of food,” explains first author Dr Bob Week, scientist in the Schulenburg group and supported by a fellowship from Kiel University’s Kiel Training for Excellence (KiTE) programme. ”In the context of the metaorganism, niche construction occurs when a host organism influences the presence of microorganisms in its environment, thereby ensuring the availability of beneficial microbes, not only during its own lifetime but possibly also during the next generation. Such niche construction of the environmental microbiome can thus mediate the successful transmission of microbiome-dependent functions from one host generation to the next, as an important prerequisite for the microbiome’s influence on host evolution.” emphasizes Week.

Creating new theoretical foundations for empirical research
In addition to the example described, the new publication highlights a total of four theoretical frameworks that show particular promise for enhancing our understanding of host-microbiome evolution. “In order to better capture the biological diversity of these systems and enable experimental testing, the frameworks we have now presented should be carefully expanded in close collaboration with colleagues working empirically,” emphasises Schulenburg, who is also active within the priority research area Kiel Life Science (KLS). “This is exactly one of the research foci of our CRC 1182. And with our new publication, we now provide critical theoretical building blocks that should stimulate novel research on the evolutionary consequences of host-microbiome associations in the future.”

Original publication:
Bob Week, Shelbi L. Russell, Hinrich Schulenburg, Brendan J. M. Bohannan and Marjolein Bruijning (2025): Applying Evolutionary Theory to Understand Host-Microbiome Evolution: New Tricks for Old Dogs. Nature Ecology & Evolution
First published: 8. September 2025 DOI: 10.1038/s41559-025-02846-w

Images are available for download:
www.uni-kiel.de/de/pressemitteilungen/2025/147-week-natecoevo.jpg
Caption: Dr Bob Week and an international research team propose further development of existing evolutionary theory to better understand the interconnected evolution of host organisms and microorganisms.
© Christian Urban, Kiel University

Contact:
Prof. Hinrich Schulenburg,
Evolutionary Ecology and Genetics (Head),
Zoological Institute, Kiel University:
Phone: +49 431-880-4143
Email: hschulenburg@zoologie.uni-kiel.de

Dr Bob Week,
Evolutionary Ecology and Genetics,
Zoological Institute, Kiel University:
Email: bweek@zoologie.uni-kiel.de

More information:
Evolutionary Ecology and Genetics,
Zoological Institute, Kiel University:
www.uni-kiel.de/zoologie/evoecogen

Environmental Studies and Biology (Bohannan Lab),
Institute of Ecology and Evolution,
University of Oregon, Eugene:
pages.uoregon.edu/bohannanlab

Kiel Training for Excellence (KiTE)-Programme,
Graduate Centre, Kiel University:
www.uni-kiel.de/de/forschung/wissenschaftlicher-nachwuchs/kite

Priority research area Kiel Life Science (KLS),
Kiel University:
www.kls.uni-kiel.de