EAGER: Testing the Host-Microbiome Specificity Paradigm in Birds

生活在动物身上和动物体内的微生物--微生物群--以许多已知和未知的方式影响它们的宿主。了解动物与其微生物群之间的关系需要我们使用正确的工具并收集适当的数据。目前，大多数脊椎动物微生物组研究有两个共同点。他们使用一种单一的标记(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，因为收集粪便很容易，而且不会致命。这两个因素可能会给微生物组的分析带来偏差和/或误差。此外，偏差/误差的数量和影响可能取决于动物宿主，因为它们有独特的自然历史和生态环境。这项研究将使用上述标准方法评估鸟类与其微生物群之间的关系，并将它们与额外的标记和采样材料进行比较。这些测试将一起展示和比较标准和更新颖的方法在研究宿主-微生物组关系方面的效用。这个项目将支持研究生和本科生的培训。在动物微生物群中，一个似乎很常见的趋势是，关系越近的动物有更相似的微生物群。哺乳动物是脊椎动物微生物群中研究得最好的一组，它们倾向于遵循这一范式，而鸟类中宿主和微生物群之间的特异性较弱。这项研究的目的是检验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更多地构成了鸟类微生物组，而不是分类组成。这将通过比较鸟枪元基因组数据(功能)和16S rRNA扩增子文库(分类组成)来进行测试。假设2是鸟类调节粘液微生物组，使其含有比管腔内容物更高的驻留细菌与暂住细菌的比率。这将通过物理分离腔内容物和粘液相关细菌来进行测试。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史联系起来。总之，这些假设是对鸟类宿主-微生物组专一性的可靠测试，并将确定常用微生物组方法的适当性。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.