EAGER: Testing the Host-Microbiome Specificity Paradigm in Birds

生活在动物身上和体内的微生物群——微生物组——以许多已知和未知的方式影响它们的宿主。理解动物和它们的微生物群之间的关系需要我们使用正确的工具和收集适当的数据。目前，大多数脊椎动物微生物组研究有两个共同点。他们使用单一标记（称为“16S”，因为它对16S rRNA基因的一部分进行测序）来识别微生物组的成员，他们经常依赖粪便作为采样材料，因为它很容易收集且不致命。这两个因素可能会在微生物组分析中引入偏差和/或误差。此外，偏差/误差的数量和影响可能取决于动物宿主，因为它们具有独特的自然历史和生态。本研究将使用上述标准方法评估鸟类与其微生物组之间的关系，并将其与其他标记物和采样材料进行比较。这些测试将共同展示和比较标准方法和更新颖的方法在研究宿主-微生物组关系方面的效用。该项目将支持学生的研究生和本科生培训。在动物微生物组中，一个似乎很常见的趋势是，关系更密切的动物有更多相似的微生物组。哺乳动物是研究得最好的脊椎动物微生物组，往往遵循这种模式，而鸟类宿主和微生物组之间的特异性较弱。本研究的目的是测试关于微生物组数据中潜在噪声源的两个假设。假设1是微生物组的功能特征比分类组成更能构成鸟类微生物组。这将通过将shotgun宏基因组数据（功能）与16S rRNA扩增子文库（分类组成）进行比较来验证。假设2是鸟类调节粘液微生物群，使其含有比管腔内容物更高的常驻细菌与瞬时细菌的比例。这将通过物理分离管腔内容物和黏液相关细菌来测试。比较分析，包括系统发育比较方法，将把鸟类微生物组数据与宿主生态和进化历史联系起来。总之，这些假设是对鸟类宿主-微生物组特异性的有力测试，并将确定常用微生物组方法的适用性。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。

The collections of microorganisms that live on and inside animals - the microbiome - affect their hosts in many known and unknown ways. Understanding the relationship between animals and their microbiomes requires that we use the right tools and collect appropriate data. Currently, most vertebrate microbiome studies have two things in common. They use a single marker (called “16S”, because it sequences a portion of the 16S rRNA gene) to identify the members of the microbiome and they frequently rely on feces as the sampling material because it is easy and non-lethal to collect. These two factors may be introducing bias and/or error into the analyses of the microbiome. Additionally, the amount and impact of the bias/error may depend on the animal host, because they have unique natural histories and ecologies. This research will assess the relationship between birds and their microbiomes using the standard methods above and compare them to additional markers and sampling material. Together these tests will demonstrate and compare the utility of standard and more novel approaches to studying the host-microbiome relationship. This project will support student graduate and undergraduate training.One trend that appears to be common in animal microbiomes is that more closely related animals have more similar microbiomes. Mammals, the best studied group of vertebrate microbiomes, tend to adhere to this paradigm, whereas the specificity between host and microbiome is weaker in birds. The objective of this research is to test two hypotheses about potential sources of noise in microbiome data. Hypothesis 1 is that functional traits of the microbiome are structuring the avian microbiome more than taxonomic composition. This will be tested by comparing shotgun metagenomic data (function) to 16S rRNA amplicon libraries (taxonomic composition). Hypothesis 2 is that birds regulate the mucus microbiome such that it contains a higher resident to transient bacteria ratio than the lumen contents. This will be tested by physically separating the lumen contents and mucus-associated bacteria. Comparative analyses, including phylogenetic comparative methods, will relate avian microbiome data to host ecology and evolutionary history. Together, these hypotheses are a robust test of host-microbiome specificity in birds and will determine the appropriateness of commonly used microbiome methods.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.