Microorganisms are increasingly recognized as ecosystem-relevant components because they affect the population dynamics of hosts. Functioning at the interface of the host and pathogen, skin and gut microbiomes are vital components of immunity. Recent work reveals a strong influence of biotic and abiotic environmental factors (including the environmental microbiome) on disease dynamics, yet the importance of the host–host microbiome–pathogen–environment interaction has been poorly reflected in theory. We use amphibians and the disease chytridiomycosis caused by the fungal pathogen Batrachochytrium dendrobatidis to show how interactions between host, host microbiome, pathogen, and the environment all affect disease outcome. Our review provides new perspectives that improve our understanding of disease dynamics and ecology by incorporating environmental factors and microbiomes into disease theory.

由于微生物会影响宿主的种群动态，因此人们越来越多地将其视为与生态系统相关的组成部分。皮肤和肠道微生物组在宿主和病原体的界面上起作用，是免疫力的重要组成部分。最近的工作揭示了生物和非生物环境因素（包括环境微生物组）对疾病动力学的强烈影响，但理论上很少反映宿主-宿主微生物组-病原体-环境相互作用的重要性。我们使用两栖动物和由真菌病原体Batrachochytrium dendrobatidis引起的乳糜菌病展示宿主，宿主微生物组，病原体和环境之间的相互作用如何影响疾病结果。我们的综述提供了新的观点，通过将环境因素和微生物组纳入疾病理论来增进我们对疾病动力学和生态学的理解。