Microbiome making you prone to IBD? Scientists find new epigenetic marker that says so.

New research is edging closer to helping us prevent IBD. By investigating the microbiome and epigenetics, scientists have discovered a new marker that could be used to lower risk of developing IBD – and even treat it. 

By Sofia Popov

Inflammatory bowel disease (IBD) affects over 1.4 million people in the United States – alone. This poses a tremendous societal challenge, not to mention the personal turmoil and struggles individuals face: everything from diarrhea, abdominal pain to bloody stools and excessive weight loss. With increased severity, the inflammation can unfold into Ulcerative Colitis and Crohn’s disease.

Numerous factors affect IBD pathogenesis, with both environment and genetics at play.

Numerous factors affect IBD pathogenesis, with both environment and genetics at play1. Still, inflammation along the digestive tract, as well as abnormal immune responses, are defining features. More on the mechanistic details remains to be uncovered. At the moment, therapeutics focus on managing inflammation and, although they can help suppress symptoms, complete treatment is still rare and many complications tend to arise2

The reality of the situation led researchers to investigate. By focusing on improving their understanding of IBD triggers, they’re looking to develop personalised approaches that can predict therapy responses and fully treat it. 

The Microbiome & IBD: An Interesting Relationship

Recently, a group of researchers investigated the relationship between the microbiome and epigenetics, seeking to see how it affects the development of IBD. Their main focus was on histone methylation, a process that controls gene expression by adding methyl groups onto DNA. Using ChIP-seq – an epigenetic technique that analyzes protein-DNA interactions- they examined the intestinal epithelial cells of recently diagnosed IBD patients. Turns out, there were higher levels of histone methylation in certain genes linked with metabolism, immune regulation and cell signalling. They believe this may open possibilities into understanding what mechanisms cause severe inflammation and even Crohn’s.

In IBD, patients present with an altered microbiome that also affects histone methylation levels.

Typically, the gut microbiome regulates these genes. In IBD, patients present with an altered microbiome that also affects histone methylation levels. Specifically, they cited higher levels of H3K4me3 (H3-lysine 4 trimethylation) at the promotor region of the DNA, proposing this as a potential marker for severe inflammation. 

Gut Health is Central to Supporting IBD

Ultimately, gut health plays a central role in which epigenetic switches are activated in IBD. It seems the microbiome actually triggers epigenetic changes that makes some people more prone to intestinal inflammation. At an individual level, the microbiome is driven by both genetics and lifestyle factors – such as diet, lineage, etc. With millions of microbes residing in our guts, how smooth our body runs surely depends on how we support them. 


  1. Renz H, von Mutius E, Brandtzaeg P, Cookson WO, Autenrieth IB, Haller D. Gene-environment interactions in chronic inflammatory disease. Nat Immunol. 2011;12(4):273–277.
  2. Kopylov U, Seidman E. Predicting durable response or resistance to antitumor necrosis factor therapy in inflammatory bowel disease. Therap Adv Gastroenterol. 2016;9(4):513–526.
  3. Theresa Alenghat (2018) Microbiota-sensitive epigenetic signature predicts inflammation in Crohn’s disease. JCI Insight, 3 (18).


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