For the thousands of people in the U.S. who suffer daily from Crohn’s disease, treatments mainly target the symptoms, with no known cure. One reason for the limited relief from this chronic and painful type of inflammatory bowel disease is the fact that its exact cause is unknown.

However, the results of a new study that reveals which gut bacteria are involved in Crohn’s disease could provide targets for future treatments, as well as better ways to diagnose the condition.

"These findings can guide the development of better diagnostics," said senior author Dr. Ramnik Xavier of Massachusetts General Hospital and the Broad Institute at the Massachusetts Institute of Technology (MIT) and Harvard University in a press release. "More importantly, our study identified specific organisms that are abnormally increased or decreased in disease, which forms a blueprint to develop microbial therapeutics."

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Gut Bacteria Differ in Crohn’s Disease

Researchers examined tissue samples taken from the intestines of 447 children and adolescents newly diagnosed with Crohn’s disease to determine how the bacteria in their intestines differed from those found in 221 people with non-inflammatory gut conditions like diarrhea or general abdominal pain.

The biopsies showed that the microbial balance in the intestines was disrupted in young people with Crohn’s disease—certain beneficial microbes showed up in lesser amounts, while harmful ones flourished.

The harmful organisms that thrived in the guts of people with Crohn’s disease included ones in the same family as Salmonella and Escherichia coli, as well as several other groups of bacteria. Beneficial bacteria that were more rare included Bifidobacterium and other families of microbes.

Twenty-eight gastroenterology centers in North America participated in the study, which was published today in the journal Cell Host & Microbe. Researchers also validated their method in additional people—both adult and pediatric patients with newly-diagnosed or established Crohn's disease—for a total of 1,742 tissue samples.

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Researchers Question Antibiotic Treatments

Many symptoms of Crohn’s disease—such as abdominal pain, cramping, and severe diarrhea—are caused by inflammation of the lining of the gastrointestinal tract. Treatments are often aimed at toning down that inflammation either with anti-inflammatory or immune-suppressing drugs.

Sometimes, though, doctors prescribe antibiotics to kill off harmful bacteria and suppress the immune system in the intestines, a method that may not be effective for people with Crohn’s disease because it might make room for harmful bacteria to grow.

“Previously, antibiotics have been claimed to provide benefits for [Crohn’s disease] patients as a first-line therapy,” the researchers wrote. “However, we question this practice based on our observation that the microbial network appears [negatively disrupted] in the context of antibiotic exposure. Loss of protective microbes has the potential of triggering a proliferation of less beneficial taxa, exacerbating the inflammation.”

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Understanding Gut Bacteria May Point to New Treatments

While many people think of bacteria in the intestines as invaders, recent research has shown that these organisms play an important role in promoting health. Other studies have found a connection between the make-up of the gut’s microbial community and inflammation, obesity, depression, and other conditions.

Stemming from this understanding, doctors are trying a new type of treatment intended to restore the health of the internal ecosystem—the fecal transplant. By transferring stool samples from a healthy patient to a sick one, researchers have been able to treat a wide range of chronic intestinal problems, such as C. difficile infections, inflammatory bowel disease, and Crohn’s disease.

Studies using fecal transplants are still ongoing, but understanding which intestinal bacteria predominate in people with Crohn’s disease could help guide those, and other, types of treatments.

“This will further develop principles that are likely to govern therapeutics in [inflammatory bowel disease],” the study authors wrote, “but they will need to be carefully thought through.”

Another possible outcome of this study is a better way to diagnose patients with Crohn’s disease. In the study, the researchers found that microbes residing in tissue samples taken from the rectum were a good indicator of the disease, regardless of where the inflammation occurred.

"This finding is particularly encouraging because it creates the opportunity to use a minimally invasive approach to collecting patient samples for early disease detection," explained first author Dr. Dirk Gevers of the Broad Institute.

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