Phenomenological mathematical models	Quantitative mathematical models for extraction of patterns from large data sets (e.g. regression analysis)
Mechanistic mathematical models	Quantitative mathematical models to mechanistically describe the relationship between different components and parameters of a system
Population dynamics	Kinetics of changes of a population (e.g. composition, size), including parameters that describe these changes (e.g. replication, death). In this review, we focus on experimental approaches that use phenotypically neutral genetic tags to study pathogen and/or host cell populations
Compartmental models	Assigns populations to compartments. Members of the respective population can enter the compartment (e.g. by birth/replication, immigration) and exit from it (e.g. by death, emigration). Compartments can, for example, represent disease states, anatomical sites or stages in a pathogen’s life cycle
Bottleneck	Describes a reduction in population size due to environmental constraints. In a genetically diverse population, this will decrease its genetic diversity
Genetic diversity	Describes the number and frequency of genetic variants within a population
Genetic drift	Describes a selectively neutral change in allele frequencies in a population after a bottleneck event
Wild‐type isogenic tagged strains	Are strains that are genetically identical except for a short genetic tag that does not affect the phenotype and fitness of the strain
Metaorganism	A community of interdependent organisms often used in the context of complex microbial communities (and their hosts)