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Understanding the dynamics of multi-type microbial ecosystems remains a challenge, despite advancing molecular technologies for diversity resolution within and between hosts. Analytical progress becomes difficult when modelling realistic levels of community richness, relying on computationally-intensive simulations and detailed parametrisation. Simplification of dynamics in polymorphic pathogen systems is possible using aggregation methods and the slow-fast dynamics approach. Here, we develop one new such framework, tailored to the epidemiology of an endemic multi-strain pathogen. We apply Goldstone’s idea of slow dynamics resulting from spontaneously broken symmetries to study direct interactions in co-colonization, ranging from competition to facilitation between strains. The slow-fast dynamics approach interpolates between a neutral and non-neutral model for multi-strain coexistence, and quantifies the asymmetries that are important for the maintenance and stabilisation of diversity.

Erratum to: A slow-fast dynamic decomposition links neutral and non-neutral coexistence in interacting multi-strain pathogens