NSF PRFB FY23: Does bacterial endospore formation affect host-microbe codiversification?

该行动资助了美国国家科学基金会2023财年生物学博士后研究奖学金，研究基因组，环境和表型之间相互作用的生命规则的综合研究。该奖学金支持将以创新方式对生活规则领域作出贡献的研究员的研究和培训。动物需要肠道内的微生物来消化食物，但目前尚不清楚同一种微生物是否长期与同一种动物共存。同样不清楚的是，是什么特征使得一些微生物谱系能够与同一动物物种长期共存。这项研究将使用活的微生物和来自啮齿动物粪便的微生物DNA来观察某些微生物谱系是否会在同一动物宿主物种中存活许多代。该项目还将确定这一过程是否主要发生在缺乏帮助它们在肠道外生存的结构的微生物身上。这项研究的结果将有助于预测哪些微生物与同一动物物种长期共存。他还将制作一个在线教程，让其他科学家学习如何在其他动物微生物系统中使用这种方法。该项目将使用高通量培养和计算方法测试两个啮齿动物系统中哺乳动物和微生物的共多样化。DNA将从东南亚和北美啮齿类动物的博物馆粪便样本中提取，并测序组装细菌宏基因组组装基因组（MAGs）。从MAGs推断的细菌系统发育将用于测试与啮齿动物宿主系统发育的一致性，表明这些生物之间存在长期联系。此外，细菌将在厌氧条件下使用一套不同的生长介质从粪便中培养和分离出来。分离的细菌将被用于检测内孢子的形成，系统发育多级模型将被用于测试内孢子形成和与宿主共多样化之间的关系。鉴定共同多样化的微生物和影响这种模式的机制将提供对脊椎动物微生物群如何组装的见解。该研究员将接受培养、计算和统计技术方面的培训，同时将博物馆标本的使用扩展到宿主-微生物生态学的机械研究。通过与芝加哥大学SACNAS分会合作，招募3名本科生组成一个同行研究社区，以测试他们自己的共同多样化假设，将扩大STEM中代表性不足群体的参与。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2023, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment, and Phenotypes. The fellowship supports research and training of the fellow that will contribute to the area of Rules of Life in innovative ways. Animals need microbes in their guts to digest food, but it is unclear whether the same microbes live with the same animal species over long time periods. It is also unknown what characteristics allow some microbial lineages to live with the same animal species for a long time. This study will use live microbes and microbial DNA from rodent feces to see if certain microbial lineages stay with the same animal host species for many generations. The project will also determine if this process occurs primarily in microbes that lack structures that help them live outside the gut. Results of this fellowship will enable predictions of which microbes live with the same animal species for long time periods. The fellow will also make an online tutorial for other scientists to learn how to use this method with other animal-microbe systems. This project will test for codiversification of mammals and microbes in two rodent systems using high-throughput culturing and computational approaches. DNA will be extracted from museum fecal samples of Southeast Asian and North American rodent species and sequenced to assemble bacterial metagenome-assembled genomes (MAGs). Bacterial phylogenies inferred from the MAGs will be used to test for congruence with rodent host phylogenies, indicating a long-term association between these organisms. Additionally, bacteria will be cultured and isolated from the feces using a suite of diverse growth media under anaerobic conditions. Bacterial isolates will be assayed for endospore formation, and phylogenetic multilevel modeling will be used to test for an association between endospore formation and codiversification with the host. Identification of codiversifying microorganisms and mechanisms that affect this pattern will provide insight into how vertebrate microbiomes are assembled. The fellow will be trained in culturing, computational, and statistical techniques while extending the use of museum specimens to mechanistic studies of host-microbe ecology. Participation of underrepresented groups in STEM will be broadened through working with the University of Chicago’s SACNAS chapter to recruit 3 undergraduates to form a peer research community that will test their own codiversification hypotheses.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.