Scientists create ‘snapshot’ of how gut microbiome communicates with immune cells; could lead to IBD treatment

Finding a cure for inflammatory bowel disease (IBD) first requires a better understanding of the pathology of IBD. In a new study, a team of researchers developed a new computational model that can create a snapshot of communication between gut bacteria and the immune system. 

“Studying interkingdom connections with BEVs in a cell-type specific resolution requires multi-disciplinary expertise and various ‘omics datasets. Then you need a computational pipeline to analyse the data from different patients. Besides the actual scientific results, in the paper we introduce an open-source pipeline that others can use to analyse their data” says Dr. Tamás Korcsmáros in a press release. “We hope that what we have demonstrated here in this study will be applied by others for understanding the mechanisms how other bacterial species communicate with our cells, and how it may be altered in other diseases.”

The microbiome holds a delicate balance of microbes that, if disrupted, can create gut-related problems, including IBD. People with IBD have shown a reduced diversity in their gut microbiome with notable decreases among Bacteroides and Firmicutes bacteria. By understanding the relationship of these bacteria to immunity, the researchers believe it could be a stepping stone towards developing targeted IBD treatments.

For some time, researchers have been looking at how bacteria communicate. More specifically, they focused their attention on tiny packages called bacterial extracellular vesicles (BEVs) that are filled with various molecules that release from the cell. These vesicles can cross the gut lining and reach immune cells where they are recognized by receptors. The contents inside BEVs can trigger immune cells to react and potentially cascade into widespread effects.

The team used a prior dataset on genes that actively make proteins in 51 types of colon cells from either healthy patients or those affected by ulcerative colitis. The team looked into the cargo proteins obtained from BEVs created from Bacteroides thetaiotaomicron.

Next, the researchers combined the dataset with a computational pipeline called MicrobioLink which predicts the interactions between microbial and host proteins and how signals cause cascading signaling systems. The analysis allowed them to draw up a picture of which microbial proteins interacted with human proteins in different types of immune cells in both a healthy gut and one with IBD.

“The finding that BEVs affect the immune system’s pathways in a cell-type specific manner, and that they are altered in inflammatory bowel disease is an important step to understanding the condition, and potentially could help in developing BEVs as a therapeutic system” says Lejla Gul, lead author on the paper.

The study is published in the Journal of Extracellular Vesicles.

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