Tuesday, December 21, 2021

Island Fox Microbiome at the Smithsonian!

FIF's 2020 Research Grant recipient Dr. Alexandra DeCandia recently spoke about her work investigating the island fox microbiome

Watch the video of the program

Here's a behind the scenes look at her process extracting the DNA of different microbes from the island fox swab samples.

Dr. Allie reports: 

I inventoried over 800 swabs and over 300 blood samples collected from Channel Island foxes and island spotted skunks in 2020. I then extracted DNA and prepared samples for microbiome sequencing (a process called "library preparation"). The last step of the library preparation is cleaning the library–in essence, removing all of the DNA fragments that I don't want to ultimately sequence.

Although it may seem like a straightforward process, this took a bit of troubleshooting. After a few failed attempts, I worked with the lab manager at the Smithsonian National Zoo's Center for Conservation Genomics to learn how to run an "eGel". In this approach, you put your library in an agarose gel (which looks like a think rectangle of gelatin), run an electrical current through the gel to separate DNA fragments based on size...

(under UV light, the fragments look like glowing bands of the gel), and then pull out the band you want to sequence (in my case, fragments roughly 400 base pairs in length).

Then the DNA had to be treated to remove "gel particles and other potential contaminants."

Overall, this was a nerve-wracking process, but thankfully it worked!

Dr. Allie has submitted all seven sequencing libraries to the Princeton University Genomics Core Facility for sequencing. She reported on some preliminary findings during her "Date with a Fox" presentation. This is Fox Science at work! 

Your donations support this cutting-edge science that will provide important information regarding island fox health.  

Swab collection continues.

What is a microbiome? and Why is this important for island foxes?