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Microbiome Immunity Project Already Extending the Known Universe of Protein Structures

By: Tomasz Kosciolek, PhD
UC San Diego Center for Microbiome Innovation
7 Mar 2018   

The Microbiome Immunity Project is off to a great start on predicting the structures of hundreds of thousands of bacterial proteins within the human gut. Read about their progress and their plans in their first project update.



The Microbiome Immunity Project was created to better understand the role of the microbiome in intestinal immune response and diseases such as Type 1 Diabetes (T1D) and Inflammatory Bowel Disease (IBD). In this project, we predict structures of bacterial proteins and use this information to annotate their functions and to understand host-microbiome interactions which are responsible for the pathology of IBD and T1D. This is a massive undertaking, as the human gut microbiome has more than 2 million unique proteins, with hundreds of thousands of proteins potentially interacting with human cells. A project of this scale is only possible thanks to the power of World Community Grid.

Our Progress So Far

With your help, we have already predicted the structures of over 50,000 prioritized proteins! In the grand scheme of the 2 million unique bacterial proteins in our gut, this may not seem like a lot, but keep in mind that the experimental work to date covers only approximately 125,000 proteins. In only 6 months we have made tremendous progress by extending our universe of known protein structures by almost 28 percent!

You may have already realized that at this pace, predicting all bacterial protein structures would take years to complete. Fortunately, we don’t have to predict every single structure, because proteins can be grouped into families. These families consist of proteins with similar structures and functions, enabling a comprehensive understanding of the family’s function with only one representative member per family. Once we identify protein families of interest, we will investigate them in more detail.

In the meantime, we have adjusted our strategy on how to prioritize the predictions. Instead of looking only at bacterial genomes (genes of an individual bacterial species), we are investigating bacterial pangenomes (genes of all bacterial strains belonging to the same species). We then prioritize those pangenomes according to their prevalence between individuals in cohort studies investigating the role of microbiome in IBD and T1D. This approach enables us to have the most impact early in the project. We not only have thorough information on microbes involved in T1D and IBD specifically, but we have also expanded our knowledge of the microbiome in general.

We are now extracting information from your predictions, and during the course of the project we plan to make the data available to the public for other exciting research. We are also working on methods to improve predictions of protein functions, enabling us to find the important protein families involved in T1D and IBD among thousands of predictions we have made so far.

All this progress has been made possible thanks to your generous contributions! There is still a lot to discover about the microbiome, but with each computation that you support we are getting a step closer to having a more detailed picture of this important ecosystem inside each of our bodies and understanding IBD and T1D. So, thank you and let’s continue working together on unraveling the mysteries of microbiome!