Epigenetic Mark Found in Microbiome Could Help Prevent Digestive Disorders

person holding stomach in pain epigenetics

Maintaining a healthy diet can be incredibly difficult to do, especially with the temptations of junk food, alcohol, and sweets. Often times we are in a rush to get to plans that we’ve made, or go grab a drink after work, and we forget to prioritize putting nutritious foods in our bodies. As a result, most of us follow a western diet in our everyday lives, because the foods are more readily available (and seem to taste better).

This diet consists of a low intake of fresh fruits and veggies, and a high intake of empty carbs, red meats and saturated fats, which can throw our intestinal microbiome out of whack. Our guts contain millions of healthy bacteria that aid in digestion and keep our bodies running smoothly, but if it is not cared for with nutritious foods, it can affect our epigenetics and leave us susceptible to developing inflammatory bowel disease (IBD), type 2 diabetes, and obesity.

In a recent study published in JCI Insights, a group of researchers from the Cincinnati Children’s Hospital Medical Center sought to learn more about the relationship between the microbiome and epigenetics, how it can affect the development of IBD, and the potential therapies and treatments that can be created for those who suffer with the digestive disorder. Particularly, the team focused their efforts on histone methylation, which is an epigenetic mechanism that controls gene expression by adding methyl groups at certain sites on the DNA.

IBD occurs when there is inflammation at any part of the digestive tract, and is characterized by symptoms of diarrhea, abdominal pain, bloody stool and unintended weight loss. Severe, long-term inflammation can lead to more serious disorders like ulcerative colitis and Crohn’s disease; both of which can be treated but have no cure yet.

It is estimated that 1.6 million people in the U.S endure IBD, yet not much is known about what causes IBD, or why certain people are at a higher risk for developing severe inflammation. Current therapies are tailored more toward controlling the inflammation rather than treating the underlying mechanisms that cause it.

In this study, the researchers wanted to determine the relationship between the microbiome and the development of Chron’s Disease from IBD. They used an epigenetic technique called ChIP-seq, which analyzes protein-DNA interactions, to examine intestinal epithelial cells donated by patients recently diagnosed with IBD.

They found increased levels of histone methylation in genes associated with metabolism, immune regulation, and cell signaling, potentially uncovering the underlying mechanisms that could cause severe inflammation and ultimately Chron’s.

These genes are typically regulated by the gut microbiome, but in patients with IBD, the microbiome was altered, epigenetically affecting histone methylation levels. Specifically, they found increased levels of H3K4me3 (H3-lysine 4 trimethylation) at the promotor region of the DNA, indicating that this histone methylation mark may help explain the severe inflammation.

The study’s lead researcher Dr. Theresa Alenghat suggests that a person’s gut health plays a large role in determining which epigenetic switches are turned on or off in IBD: “This study suggests that the microbiome triggers epigenetic change that could make some individuals more prone to intestinal inflammation,” she said. “Each person’s microbiome is driven by genetics as well as external environmental factors, such as food, where we live, pets, mom’s microbiome, etc”.

Although diet is not considered to be the deciding factor in IBD and Chron’s disease, the findings in this study highlight the importance of digestive health. Dr. Alenghat hopes that future research on IBD will utilize the information on these pathways, along with the healthy bacteria we already have in our guts with hopes to create a cure and effective prevention for the underlying mechanical causes of IBD.


For more information on the influence that various foods might have on your epigenetics, please view our e-book Epigenetics in Life: What We Eat.

epigenetics diet



Source: Theresa Alenghat (2018) Microbiota-sensitive epigenetic signature predicts inflammation in Crohn’s diseaseJCI Insight, 3 (18).

Reference:  Cincinnati Children’s  “Epigenetic Signature May Help People Stay Ahead of IBD” Cincinnati Children’s Newsroom. 20 September 2018. Web.

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About Tim Barry 31 Articles
Tim received his B.S in Biology with minors in Chemistry and Business from DeSales University. He has been interested in epigenetics for over a decade and spent three summers researching DNA and Enzymes at Cold Spring Harbor Labs. He is impressed with how the dynamic nature of epigenetics can continually affect someone’s lifestyle and their future descendants. During his down time, Tim will be at the beach, playing golf, at the gym, or with his friends enjoying a fine glass of rye whiskey.

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