Collaborative Research: MIM: Gut-inhabiting fungi influence structure and function of herptile microbiomes through horizontal gene transfer and novel metabolic function

合作研究：MIM：肠道真菌通过水平基因转移和新的代谢功能影响爬行动物微生物组的结构和功能

• 批准号: 2125066
• 负责人: Jason Stajich
• 金额: $ 87万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-01-01 至 2025-12-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2125066&HistoricalAwards=false
• 关键词: Collaborative; Research; MIM; Gut; inhabiting

Reptiles and amphibians are among the most threatened species on the planet, and an increasing number of their species must be managed in captive breeding programs. Understanding the biodiversity and function of microbes that are present in the digestive tracts of reptiles and amphibians is critical for insight into their role in animal health. Early research suggests that the filamentous fungus Basidiobolus is an important member of reptile and amphibian gut microbiomes, and that this fungus influences what types of bacteria are present in the digestive tract. Genomic sequencing of the Basidiobolus fungus shows that genes have been transferred to the fungus from the gut bacteria. This transfer of genes between bacteria and fungi results in novel metabolism in the fungus that may play important roles in regulating the reptile/amphibian host’s immune system, iron metabolism, and chemical communication with the gut bacteria. An interdisciplinary scientific approach will be used to understand the functional roles that specialized metabolites play in microbial interactions between fungi and bacteria in gut microbiomes of animals and also other natural microbiomes. Outreach activities with zoos and the Great Smoky Mountains National Park will share information about reptile and amphibian gut microbiomes with the general public, and educational material will be provided to educators for inclusion in K-12 and university curricula. Interdisciplinary training of students and postdoctoral researchers to prepare them for careers in research, education, and outreach is central to the project. This work will advance a new scientific understanding of the fundamental roles that specialized metabolites play in microbial interactions between fungi and bacteria in gut microbiomes. This will be accomplished through an interdisciplinary approach combining ecology and evolutionary biology, genomics and metagenomics, natural product chemistry, synthetic microbiome experiments, and controlled amphibian feeding trials. Preliminary data reveal that fungi in the genus Basidiobolus are dominant members of the herptile microbiome, and that microbial community structure is shaped by the genetic diversity of Basidiobolus, which has acquired specialized metabolism through HGT. Integration of biological, molecular, genomic, metagenomic, and chemical resources in the proposed herptile system will allow for tests of the following hypotheses: H1: Herptile microbiomes are characterized by unique fungal communities not found in other nonpathogenic, microbiome systems. H2: The bacterial assemblages of herptile microbiomes are structured by interactions with fungi. H3: HGT from co-occurring bacteria to herptile gut fungi allowed Basidiobolus to acquire novel metabolic functions necessary to adapt to, and function in, the herptile microbiome. H4: Fungal-bacterial interactions in herptile GI systems are regulated by metabolites that influence community structure and function. H5: The phenotype of the host-microbiome association is species/context dependent. This work will further refine the general model that the animal gastrointestinal environment promotes HGT between bacteria and fungi, and that this HGT selects for specialized metabolites that modulate the host immune system (cyclic peptides), and allow fungi to function in a reduced oxygen environment and compete in a bacterial rich microbial community (siderophores and surfactins).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

爬行动物和两栖动物是地球上受威胁最大的物种之一，越来越多的物种必须在圈养的繁殖计划中进行管理。了解爬行动物和两栖动物消化道中存在的微生物的生物多样性和功能对于深入了解其在动物健康中的作用至关重要。早期的研究表明，丝状真菌basidiobolus是爬行动物和两栖动物微生物组的重要成员，并且这种真菌会影响消化系统中存在的细菌类型。基因组真菌的基因组测序表明，基因已从肠道细菌转移到真菌中。细菌和真菌之间基因的转移导致真菌中的新陈代谢，可能在调节爬行动物/两栖宿主的免疫系统，铁代谢以及与肠道细菌的化学通信方面起着重要作用。跨学科的科学方法将用于了解专门代谢产物在动物肠道微生物中真菌与细菌之间的微生物相互作用中发挥的功能作用，以及其他天然微生物。与动物园和大烟山国家公园的外展活动将与公众共享有关复制和两栖动物肠道微生物的信息，并将向教育材料提供教育材料，以在K-12和大学课程中纳入教育工作者。对学生和博士后研究人员进行研究，教育和外展职业的跨学科培训是该项目的核心。这项工作将提高对专门代谢物在肠道微生物组中真菌和细菌之间微生物相互作用中发挥的基本作用的新科学理解。这将通过结合生态学和进化生物学，基因组学和宏基因组学，自然产物化学，合成微生物组实验以及受控的两栖动物进食试验的跨学科方法来实现。初步数据表明，Basidiobolus属中的真菌是遗传学微生物组的主要成员，并且微生物群落结构是由基本obolus的遗传多样性所塑造的，Basidiobolus的遗传多样性通过HGT获得了专门的代谢。在拟议的遗传系统中的生物学，分子，基因组，元基因组和化学资源的整合将允许测试以下假设：H1：遗传学微生物组的特征是在其他非病原体，微生物组系统中发现的独特真菌群落的特征。 H2：遗传性微生物组的细菌组合是通过与真菌的相互作用结构的。 H3：HGT从共生的细菌到遗传肠真菌，允许Basidiobolus获得适应和发挥作用的新型代谢功能。 H4：Herptile GI系统中的真菌 - 细菌相互作用受影响社区结构和功能的代谢产物的调节。 H5：宿主 - 微生物组关联的表型取决于物种/背景。 This work will further refine the general model that the animal gastrointestinal environment promotes HGT between bacteria and fungi, and that this HGT selects for specialized metabolites that modulate the host immune system (cyclic peppers), and allow fungi to function in a reduced oxygen environment and compete in a bacteria rich microbial community (siderophores and surfactins).This award reflects NSF's statutory mission and使用基金会的知识分子优点和更广泛的影响审查标准，通过评估被认为是宝贵的支持。

项目成果

Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria

• DOI: 10.1128/msphere.00475-23
• 发表时间: 2024-02
• 期刊: mSphere
• 影响因子: 4.8
• 作者: Lluvia Vargas-Gastélum;Alexander S. Romer;M. Ghotbi;J. Dallas;N. Alexander;Kylie C. Moe;Kerry L. McPhail;George F Neuhaus;Leila Shadmani;J. Spatafora;J. Stajich;Javier F. Tabima;Donald M Walker