The natural microbiome of a multicellular host organism consists of bacteria, viruses, and fungi that reside in and on its body. This microbiome plays a crucial role in various essential functions including aiding food utilization and defending against pathogens. However imbalances in the microbiome are linked to numerous serious diseases.

For several years, the Collaborative Research Centre (CRC) 1182 Origin and Function of Metaorganisms at Kiel University has been exploring the intricate interactions between hosts and microorganisms and their significance in key life processes. In a recent study researchers investigated how an organism's microbiome and its surrounding microbial environment influence one another.

Researchers discovered that the microbiome of nematodes from the genus Caenorhabditis does not have a fixed, universal composition. Instead, it is highly individual and shaped by the microbial environment of its habitat. Additionally they found evidence suggesting that these worms may actively influence the microbial composition of their surroundings potentially modifying their environment to create more favorable living conditions. This was demonstrated by the fact that apples colonized by the worms exhibited a significantly different metabolome signature compared to those without them.

These new insights into the dynamic reciprocal interactions between microbiomes were recently published in the scientific journal mSystems by a research team from Kiel University’s Evolutionary Ecology and Genetics group led by Professor Hinrich Schulenburg.

Comparative Study of Nematode and Apple Microbiomes
A key question in fundamental research is how microbial communities initially establish themselves within a living organism. Scientists particularly explore whether different organisms develop a distinct stable microbiome that serves essential functions for the host.

To investigate this, the CRC 1182 research team utilizes Caenorhabditis elegans as a model organism. Since C. elegans feeds on bacteria and inhabits decaying fruit, its microbiome is heavily influenced by its immediate environment, particularly the substrate it resides in. While previous studies have examined worm microbiomes in natural substrates our research systematically compares different substrates to understand how the surrounding microbial environment shapes the microbiome composition of these animals explains Dr. Julia Johnke, first author of the study and a research associate in Professor Schulenburg’s research group.To address this unexplored aspect the research team at Kiel University examined a natural substrate and its interactions with nematodes. They studied a compost heap containing apples from an orchard. Over a two-year period we collected ten apples each week and analyzed both the microbiome of the nematodes found on them and the microbiome of the apples themselves explains Dr. Julia Johnke, a member of CRC 1182.The microbiome of C. elegans is shaped by its substrate with worms from different sources showing distinct microbiomes. Even within the same apple individual worms had unique microbial compositions confirming the absence of a core microbiome. Researchers identified dispersal limitation as a key factor as the worm’s restricted movement results in a microbiome shaped by local bacterial availability and competition. Interestingly, metabolome analysis revealed that nematodes may influence the microbial composition of apples and their metabolic processes even more than the apples influence the worms.

Source: https://www.uni-kiel.de/en/university/details/news/035-johnke-msys