The concept of fitness is often reduced to a single component, such as the replication rate in a given habitat. For species with complex life cycles, this can be an unjustified oversimplification, as every step of the life cycle can contribute to reproductive success in a specific way. In particular, this applies to microbes that spend part of their life cycles associated to a host, i.e. in a microbiota. In this case, there is a selection pressure not only on the replication rates, but also on

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... he phenotypic traits associated to migrating from the external environment to the host and vice-versa. Here, we investigate a simple model of a microbial population living, replicating, migrating and competing in and between two compartments: a host and its environment. We perform a sensitivity analysis on the global growth rate to determine the selection gradient experienced by the microbial population. We focus on the direction of selection at each point of the phenotypic space, defining an optimal way for the microbial population to increase its fitness. We show that microbes can adapt to the two- compartment life cycle through either changes in replication or migration rates, depending on the initial values of the traits, the initial distribution of the population across the compartments, the intensity of competition, and the time scales involved in the life cycle versus the time scale of adaptation (which determines the adequate probing time to measure fitness). Overall, our model provides a conceptual framework to study the selection on microbes experiencing a host-associated life cycle.