EAGER: Testing the Host-Microbiome Specificity Paradigm in Birds

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.