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

动物的“微生物群”由生活在它上面和里面的所有微生物组成。微生物群以复杂的方式与动物的免疫系统相互作用。动物如何既有高效的免疫系统，又有高度多样化的可能含有病原体的微生物群，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。这项提议将优化一种在人类身上开发的程序，称为“IgA-Seq”，用于鸟类。IGA-Seq根据每个单独的微生物是否(由宿主)标记了IgA，将微生物群分类为两个种群。然后，可以对不同的种群进行测序和分析，以确定宿主认为谁是潜在威胁，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镜头中提供微生物群的视角。这项研究涉及多个研究领域，一旦得到优化，将成为免疫系统和微生物组之间的非致命性和新的联系，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，研究人员将促进对当地小学年龄儿童的野外工作和处理野生鸟类的观察。胃肠上皮特别容易受到微生物的感染，因为脊椎动物会把微生物带到食物上的消化道，消化过程是在一个受保护和滋养的环境中进行的。脊椎动物有与肠道相关的淋巴组织和免疫机制，可以监测和管理肠道微生物群，例如用免疫球蛋白A包裹潜在的病原体。微生物是否被免疫球蛋白A标记不是随机的，可以最大限度地减少对宿主的特定威胁，而不会引起全身免疫反应或炎症，而生产成本可能很高。因此，我们可以使用IgA来更好地了解脊椎动物微生物群的生态和进化，因为它意味着宿主如何看待和管理其微生物群，以最大限度地适应宿主。这一建议的主要假设是，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因子，也是理解微生物组作为宿主特征进化的关键。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将微生物组逐个细胞分类到种群中。使用未分类的、免疫球蛋白A阳性(IgA+)和免疫球蛋白A阴性(IgA-)的细胞种群将识别“核心”微生物群，并量化微生物分类群和微生物功能在个体和物种内部和之间的持久性。该奖项反映了NSF的法定使命，并通过使用基金会的智力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.