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The Microbiome Immunity Project Must Go On!
By: The Microbiome Immunity Project research team
11 May 2020   

Summary
Research in the time of a pandemic is more important than ever. Here’s how the Microbiome Immunity Project team is making continued progress while working from home.

 

Trillions of bacteria live inside and on our bodies. The Microbiome Immunity Project is using the computational power of World Community Grid to study the proteins produced by these bacteria, which are encoded in their genomes. This helps scientists understand the role of the microbiome in disease.

We want to thank all of our volunteers for their help with donating valuable computer time! So far, we have run more than 300,000 protein sequences through our pipeline. With the predicted models and our new method for functional annotation, we have finally started a deeper dive into analyzing our data!

The Context

The Microbiome Immunity Project spring meeting was virtual instead of in-person this year.  
Top row (left to right): Mary Maranga, Richard Bonneau, Tomasz Kościółek
Middle row (left to right): Julia Koehler Leman, Paweł Szczerbiak, Daniel Berenberg
Bottom row (left to right): Douglas Renfrew, Vladmir Gligorijevic, Chris Chandler
Not pictured: Tommi Vatanen

We were supposed to meet in New York City in March for our regular research general meeting. However, due to the COVID-19 pandemic, this meeting could not happen in person. Instead, we had several-hour long video calls through Zoom on those three days, March 18-20. Researchers from the USA (New York), Poland, and New Zealand participated in the meeting. Finding a time that worked for everyone in those three different time zones across the globe was hard, but we pulled it off. 

The Progress

Our paper about functional annotation from sequence and structure (you can check out a preprint here) has been submitted and is currently under review. We’re keeping our fingers crossed for positive reviews! 

We are also working on two more papers that dive into the data collected throughout this project, both experimental and our predictions. For this, we started working on a database that makes this data easily accessible and analyzable to us as a group, and later to the general scientific community and to all of you! Much work is still to be done, but let us assure you that we are making progress. To tackle these challenges, we also have some new members in our group that can help us. The Polish team is getting bigger by an additional graduate student and postdoctoral fellow and our NYC team has another software engineer who helps us with setting up the databases. Welcome to our team: Paweł, Mary, and Chris. 

In other milestone news, research team member Bryn Taylor successfully defended her PhD thesis on April 14. In keeping with the times, her defense was conducted via Zoom which meant that a large group of family, friends, and colleagues could attend. Congratulations, Dr. Taylor!

Our research activities have always involved remote work and online communication. In these trying times we are working as hard as ever, and we are hoping that all World Community Grid volunteers are taking measures to stay safe and healthy. We thank you for your continued support!