Collaborative Research: Linking Causes of Variation in the Amphibian Skin Microbiome with Consequences for Disease Risk

动物体内和身上都生活着微生物群落(细菌、病毒、真菌)。这些微生物群落被称为共生微生物群落，或微生物组。共生微生物群落日益被认为是人类和动物健康的重要参与者。共生微生物通过影响宿主对致病微生物(病原体)的反应，可能对动物(宿主)的健康很重要。本项目旨在了解微生物组如何影响抗病能力，同时研究寄生真菌病，这是一种由病原体巴氏杆菌(Batrachochytrium Dendrobatidis，简称Bd)引起的两栖动物(青蛙、蟾蜍和火蜥蜴)的毁灭性疾病。BD是一种真菌，可以感染两栖动物的皮肤，并可能导致潜在的致命性丝状真菌病。内华达山脉黄腿蛙(Rana Sierrae)濒临灭绝，Bd是这种青蛙最严重的威胁之一。BD已经导致了整个种群的大规模死亡。然而，某些种群似乎对致死性的旋毛菌病有一定的抵抗力。了解为什么这些耐药种群能够在Bd感染的情况下存活下来，可能对保护该物种的努力至关重要。尽管缺乏确凿的证据，但皮肤微生物群可能对疾病抵抗力有贡献。这个项目将解决三个核心问题：(1)青蛙皮肤微生物群在多大程度上有助于抗病？(2)当青蛙感染Bd时，微生物群的组成(即组成微生物群的微生物物种)是否会影响微生物群的稳定性？这对于理解当宿主受到传染病威胁时微生物组的持续功能可能是重要的。(3)宿主和环境的差异如何影响微生物组的组装？换句话说，是什么力量导致了不同青蛙或种群的微生物群落的差异，或者是同一只青蛙在不同的时间内的微生物群落的差异？这可能揭示了形成微生物组功能差异的潜在原因，例如抗病能力的差异。总之，这项工作将促进对宿主和环境如何决定微生物组组成以及这反过来如何塑造微生物组功能和稳定性的理解。对这些过程的了解与保护受威胁的两栖动物的战略有关。更广泛地说，了解西耶雷微生物群是如何与Bd相互作用的，可以为深入了解微生物与病原体的相互作用以及其他动物和人类的传染病管理提供见解。共生微生物群落越来越被认为是多细胞生物体发展和健康的重要参与者。几项研究发现，病原微生物引起的疾病与宿主微生物组的组成与健康人的微生物区系相比发生变化有关，但往往很难确定因果关系：观察到的相关性可能表明特定的微生物组组合赋予疾病抵抗力，或者病原体感染扰乱和改变了微生物组。该项目旨在了解两栖动物皮肤相关细菌群落(皮肤微生物群)在介导对真菌病原体树枝状巴氏杆菌的抗性中的作用。该项目将测试抗病和敏感宿主之间是否存在微生物组差异，这暗示了自然界的保护作用。重要的是，这项工作将通过测试微生物组的实验改变是否导致抗病能力的变化，或者病原体感染是否改变微生物组，进一步阐明病原体和微生物组之间的因果关系。这项研究还旨在了解是什么决定了微生物组的系统发育和功能组成，这一问题是理解微生物组相关抗病差异的根源的基础。现场调查将被用来量化宿主遗传变异和环境因素与从野生青蛙采集的皮肤微生物组的系统发育和功能组成之间的关联程度，而实验操作将清楚地显示这些关系中的因果关系。将开发数学模型，以确定潜在驱动微生物群落组成变化的生态机制。最后，将结合群落组装和抗病概念，开发干扰条件下(如病原体感染)微生物群落动态的预测模型。

Animals have communities of microbes (bacteria, viruses, fungi) living in and on their bodies. These microbial communities are referred to as symbiotic microbial communities, or the microbiome. Symbiotic microbial communities are increasingly recognized as important players in the health of humans and animals. Symbiotic microbes may be important to animal (host) health by affecting host response to disease-causing organisms (pathogens). This project aims to understand how the microbiome affects disease resistance while studying chytridiomycosis, a devastating disease of amphibians (frogs, toads and salamanders) caused by the pathogen Batrachochytrium dendrobatidis (abbreviated Bd). Bd is a fungus that infects the skin of amphibians and can cause potentially-lethal chytridiomycosis. The Sierra Nevada yellow-legged frog (Rana sierrae) is in danger of extinction and Bd is one of the most serious threats to this frog. Bd has caused massive die-offs of entire populations of R. sierrae. However, certain populations of R. sierrae appear to be somewhat resistant to lethal chytridiomycosis. Understanding why these resistant populations are able to survive despite Bd infection may be critical for efforts to conserve the species. It is possible that the skin microbiome contributes to disease resistance, however definitive evidence is lacking. This project will address three core questions: (1) To what extent does the R. sierrae skin microbiome contribute to disease resistance? (2) Does microbiome composition (i.e., the microbial species that make up the microbiome) affect the stability of the microbiome when frogs become infected with Bd? This may be important to understanding continued functionality of the microbiome when the host is threatened by infectious diseases. (3) How do host and environmental differences affect microbiome assembly? In other words, what are the forces that lead to differences in the microbiome of different frogs or populations, or within an individual frog at different times? This may reveal underlying causes that shape functional variation attributed to the microbiome, such as differences in disease resistance. In summary, this work will advance understanding of how host and environment determine microbiome composition and how this in turn may shape microbiome function and stability. Understanding of these processes is relevant to strategies for protecting threatened amphibians. More broadly, understanding how the R. sierrae microbiome interacts with Bd can provide insights into microbiome-pathogen interactions and management of infectious disease in other animals and humans.Symbiotic microbial communities are increasingly recognized as important players in the development and health of multicellular organisms. Several studies have found that disease caused by pathogenic microbes is associated with changes in the composition of the microbiome of the host compared with the microflora of healthy individuals, but it has often been difficult to determine cause and effect: the observed correlation may indicate that particular microbiome assemblages confer disease resistance, or that pathogen infection disrupts and alters the microbiome. This project aims to understand the role of the amphibian skin-associated bacterial community (skin microbiome) in mediating resistance to the fungal pathogen Batrachochytrium dendrobatidis. The project will test if microbiome differences exist between disease-resistant and -susceptible hosts, suggestive of a protective role in nature. Importantly, this work will further clarify the causal relationship between pathogen and microbiome by testing if experimental alteration of the microbiome leads to changes in disease resistance, or if instead pathogen infection alters the microbiome. This study also aims to understand what determines the phylogenetic and functional composition of the microbiome, a question that is fundamental to understanding the root of microbiome-associated differences in disease resistance. Field surveys will be used to quantify the degree to which host genetic variation and environmental factors are associated with the phylogenetic and functional composition of the skin microbiome sampled from wild frogs, while experimental manipulations will clearly show cause and effect in these relationships. Mathematical models will be developed to identify ecological mechanisms that potentially drive variation in microbial community composition. Finally, predictive models of microbial community dynamics under conditions of disturbance (such as pathogen infection) will be developed, integrating community assembly and disease resistance concepts.