Using the immune system to understand vertebrate-microbiome interactions and evolution

动物的“微生物组”由生活在动物身上和体内的所有微生物组成。微生物组以复杂的方式与动物的免疫系统相互作用。动物既拥有高效的免疫系统，又拥有可能含有病原体的高度多样化的微生物群，这是通过对检测到的威胁有不同反应的适应性免疫来实现的。免疫系统的一项工作是监测动物肠道中的微生物，并通过用免疫球蛋白A （IgA）标记潜在病原体来阻止它们进入血液。这一提议将优化人类开发的一种名为“IgA-Seq”的程序，以应用于鸟类。IgA- seq根据每个微生物是否被（宿主）标记为IgA，将微生物组分为两类。然后可以对不同的种群进行测序和分析，以确定宿主将谁视为潜在威胁，以及这些潜在威胁具有哪些基因。完成这项研究将从宿主免疫系统的角度提供对微生物组的看法。这项研究对多个研究领域都有影响，一旦得到优化，将成为免疫系统和微生物组之间的一种非致命性的新联系，可用于野生动物研究。为了促进未来的研究，研究人员将制作整个过程的视频教程。为了促进下一代的研究，研究人员将协助当地小学儿童实地观察和处理野生鸟类。胃肠道上皮特别容易受到微生物感染，因为脊椎动物通过食物将微生物带入消化道，而消化过程是在受保护和滋养的环境中进行的。脊椎动物有肠道相关的淋巴组织和免疫机制来监测和管理肠道微生物群，比如用免疫球蛋白a覆盖潜在的病原体。是否用IgA标记微生物不是随机的，并且在不引起全身免疫反应或炎症的情况下最大限度地减少对宿主的特定威胁，而这可能是昂贵的。因此，我们可以利用IgA来更好地了解脊椎动物微生物群的生态学和进化，因为它表明宿主如何看待和管理其微生物群以最大化宿主的适应性。该建议的主要假设是宿主免疫系统（通过IgA）与共生肠道微生物组之间的相互作用是宿主-微生物组动力学的中心调节器，也是理解微生物组作为宿主特征的进化的关键。为了解决这一假设，我们提出了一个初步的研究目标：优化在人类中开发的IgA- seq方法，该方法根据是否附着IgA将微生物组逐细胞分类到群体中。使用未分类的IgA阳性（IgA+）和IgA阴性（IgA-）细胞群将确定“核心”微生物组，并量化个体和物种内部和之间微生物分类群和功能的持久性。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。

An animal’s “microbiome” consists of all the microorganisms that live on and inside it. The microbiome interacts with the animal’s immune system in complex ways. How an animal has both a highly effective immune system, but also a highly diverse microbiome that potentially contains pathogens, is achieved through adaptive immunity that has variable responses to detected threats. One job of the immune system is to monitor the microbes in an animal’s gut and to stop potential pathogens from crossing over into the blood by tagging them with immunoglobulin A (IgA). This proposal will optimize a procedure developed in humans, called “IgA-Seq”, for application to birds. IgA-Seq sorts a microbiome into two populations, based on whether or not each individual microbe has been tagged with IgA (by the host). The separate populations can then be sequenced and analyzed, to determine who the host sees as a potential threat and what genes those potential threats have. Completing this research will provide a view of the microbiome from the lens of the host’s immune system. This research has implications for multiple fields of study and, once optimized, will be a non-lethal and novel link between the immune system and the microbiome, for use in wild animal studies. To promote future research, the researchers will create video tutorials of the entire process. To promote future generations of research, the researchers will facilitate observations of the field work and handling of wild birds by local elementary aged children. The gastrointestinal epithelium is especially vulnerable to microbial infection, because vertebrates bring microbes into their digestive tract on food and the process of digestion occurs in a protected and nourishing environment. Vertebrates have gut-associated lymphoid tissue and immunological mechanisms that monitor and manage the gut microbiome, such as coating a potential pathogen with Immunoglobulin A. Whether a microbe is tagged with IgA is not random and minimizes specific threats to the host without causing a systemic immune response or inflammation, which can be costly to produce. Therefore, we can use IgA to better understand the ecology and evolution of the vertebrate microbiome because it signifies how the host views and curates its microbiome to maximize host fitness. The primary hypothesis of this proposal is that the interaction between the host’s immune system (via IgA) and the commensal gut microbiome is a central regulator of host-microbiome dynamics and key to understanding the evolution of the microbiome as a trait of the host. To address this hypothesis, we propose one initial research aim: optimize the method IgA-Seq, developed in humans, that sorts a microbiome cell-by-cell into populations based on whether an IgA is attached. Using unsorted, IgA positive (IgA+) and IgA negative (IgA-) cell populations will identify the “core” microbiome and quantify persistence of microbial taxa and functions within and across individuals and species.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.