The Individual Microbiome – More Chance Than Selection

The microbial community appears not to be subject to any evolutionary selection process

All living beings live in symbiosis with an abundance of micro-organisms – the microbiome – that settle on and in their tissues. Researchers at the Max Planck Institute for Evolutionary Biology in Plön and the University of Kiel have compared the microbiome compositions of different animal species with model calculations. They discovered that the microbiomes of some species are largely composed in a way that can be expected without selection pressure. The species in many microbiomes are therefore mainly randomly distributed. In contrast, some bacteria appear more frequently than predicted by random models; these presumably have key functions for the survival of the organism.

The researchers from Kiel have investigated how the microbiome composition of an organism develops. It is unclear whether the microbial community is subject to a selection process or whether the composition is more or less random. Using neutral null models, the scientists have calculated microbiomes as they would arise in the absence of selection. They then compared these microbiomes with the actual microbial communities of various animals such as sponges, jellyfish, nematodes, and mice.

In many organisms, the real and theoretical data agree surprisingly well. “The predicted composition in the house mouse, for example, is also found in the actual microbial community”, says Michael Sieber from the Max Planck Institute for Evolutionary Biology. Selection may therefore play a less important role in the individual microbiome composition than previously assumed. “This does not mean that the microbiome has no important functions for the organism. However, it could be an indication that many different microbiome compositions can fulfil these functions equally well. Which of these different possible compositions actually develops in a single organism is largely coincidental”, explains Sieber.

In addition to a high degree of agreement between the theoretical and actual composition, the researchers also found significant differences. Individual bacteria species in the mouse microbiome deviate considerably from the prediction. Some of these bacteria are involved in digestion, for example. Their occurrence may therefore be the result of a targeted selection process. The collective microbial species composition in the nematode Caenorhabditis elegans also hardly matches the calculated compositions. Because of its rapid generational changes, the nematode may not live long enough to develop a stable, largely neutral microbiome.

“The deviations between model and reality in animals such as mice likely indicate special functions of certain microorganisms. These species may therefore have key functions for the survival of the organism”, explains Sieber.