Modelling the ecology of host-associated microbiomes

The study of microbes associated with animals, plants, and fungi – here referred to as host-associated microbiome – is one that is modifying our understanding of ecology and evolution. While empirical evidence has accumulated rapidly, the theory to explain it has been lagging behind. In this thesis, I present my contribution to understanding the effect of host-specific ecological processes on the microbiome.

Each chapter is focused on a specific process with eco-evolutionary consequences. To gain certainty about our understanding, I simplify the complex biology of real-world hosts and microbes. In the models, hosts only provide a space for microbes to inhabit without being affected by them. On the other hand, the microbiome is affected by the processes imposed by their hosts – specifically the microbial composition. I rely on the theory of stochastic processes and focus on birth, death, and immigration as the drivers of the microbial dynamics.

The first project stems from observing that compared to classical habitats, hosts have a lifespan that might interfere with the microbial dynamics. For hosts which acquire all their microbes from the environment, the lifespan indeed interferes in the long run, even leading to the coexistence of subpopulations with distinct microbiome. In the second project I address the possible "inheritance" of microbes from parents to their newborn hosts. I observe that its effects depend on life-history traits including immigration and host lifespan. In the last project, I question one of the critical assumptions. Rather than equal growth and death rates for all microbes, I assume differences in a simplified model. I find a surprising result – regardless of the assumption on these rates, if immigration and biodiversity are sufficiently large, differences at the population level do not modify the emergent community pattern.



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