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 coexistence (endemic infection) or host population extirpation (epidemic infection). Diversity and composition of skin-associated bacteria differed between populations of the frog, Rana sierrae, that coexist with or were extirpated by the fungal pathogen, Batrachochytrium dendrobatidis (Bd). 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 did not vary. This result suggests that pathogen infection shapes variation in the skin microbiome across host populations that coexist with or are driven to extirpation by the pathogen. By contrast, microbiome richness was largely unaffected by pathogen infection intensity, but was strongly predicted by geographical region of the host population, indicating the importance of environmental or host genetic factors in shaping microbiome richness. Thus, while both richness and composition of the microbiome differed between endemic and epidemic host populations, the underlying causes are most likely different: pathogen infection appears to shape microbiome composition, while microbiome richness was less sensitive to pathogen-induced disturbance. Because higher richness was correlated with host persistence in the presence of Bd, and richness appeared relatively stable to Bd infection, microbiome richness may contribute to disease resistance, although the latter remains to be directly tested.

传染病对人类与野生动物种群均造成严重危害，但即便同一宿主物种的不同个体或种群，疾病所产生的影响也可能存在显著差异。明确此类差异的成因，是理解疾病传播动态、缓解传染病危害的核心要点，但在自然暴发的疫情中厘清因果关系与相关性却极具挑战。本研究旨在探究共生细菌群落与传染病之间的关联，通过监测病原体入侵前后的多个宿主种群，以推断二者间潜在的因果联系。研究结果显示，共生细菌与病原体感染的两种截然不同的转归密切相关：宿主与病原体共存（地方性感染），或是宿主种群彻底消亡（流行性感染）。与真菌病原体蛙壶菌（Batrachochytrium dendrobatidis, Bd）共存或被其导致种群灭绝的内华达山蛙（Rana sierrae）种群中，皮肤共生细菌的多样性与群落组成均存在显著差异。研究借助病原体入侵前后多个蛙种群的采样数据，推断真菌病原体与共生细菌之间的因果关系。在宿主种群间，皮肤微生物组的群落组成差异最显著的预测因素为病原体感染严重程度，即便在感染转归未发生变化的分析中亦是如此。这一结果表明，病原体感染塑造了那些与病原体共存或被其逼至灭绝的宿主种群的皮肤微生物组差异。与之相反，微生物组的丰富度基本不受病原体感染强度的影响，却由宿主种群的地理区域所显著决定，这表明环境或宿主遗传因素在塑造微生物组丰富度中发挥着关键作用。因此，尽管地方性感染与流行性感染的宿主种群间，微生物组的丰富度与群落组成均存在差异，但其背后的成因大概率各不相同：病原体感染似乎主导了微生物组群落组成的变化，而微生物组丰富度对病原体引发的干扰则相对不敏感。由于更高的微生物组丰富度与宿主在蛙壶菌感染下的存续能力呈正相关，且丰富度在蛙壶菌感染过程中相对稳定，因此微生物组丰富度或有助于提升宿主的疾病抗性，不过这一结论仍需通过直接实验验证。