Data from: Epidemic and endemic pathogen dynamics correspond to distinct host population microbiomes at a landscape scale

Infectious diseases have serious impacts on human and wildlife populations, but the effects of a disease can vary, even among individuals or populations of the same host species. Identifying the reasons for this variation is key to understanding disease dynamics and mitigating infectious disease impacts, but disentangling cause and correlation during natural outbreaks is extremely challenging. This study aims to understand associations between symbiotic bacterial communities and an infectious disease, and examines multiple host populations before or after pathogen invasion to infer likely causal links. The results show that symbiotic bacteria are linked to fundamentally different outcomes of pathogen infection: host-pathogen co-existence (endemic infection) or host population extirpation (epidemic infection). Diversity and composition of skin-associated bacteria differed between populations of the frog, Rana sierrae, that co-exist with or were extirpated by the fungal pathogen, Batrachochytrium dendrobatidis. Data from multiple populations sampled before or after pathogen invasion were used to infer cause and effect in the relationship between the fungal pathogen and symbiotic bacteria. Among host populations, variation in the composition of the skin microbiome was most strongly predicted by pathogen infection severity, even in analyses where the outcome of infection was held constant. This result suggests that pathogen infection shapes variation in the skin microbiome across host populations that co-exist with or are driven to extirpation by the pathogen. In contrast, microbiome richness was largely unaffected by pathogen infection intensity, but was strongly predicted by geographic region of the host population, indicating the importance of environmental or host genetic factors in shaping microbiome richness.