The researchers led by Case Western Reserve University School of Medicine in the US also linked a new bacterium to the previous bacteria associated with Crohn's.
"We already know that bacteria, in addition to genetic and dietary factors, play a major role in causing Crohn's disease," said the study's senior author, Mahmoud A Ghannoum, from Case Western Reserve and University Hospitals Cleveland Medical Centre.
"While most researchers focus their investigations on these bacteria, few have examined the role of fungi, which are also present in everyone's intestines," he said.
The groundbreaking findings could lead to potential new treatments and ultimately, cures for the debilitating inflammatory bowel disease, which causes severe abdominal pain, diarrhea, weight loss and fatigue, researchers said.
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"It can result in a new generation of treatments, including medications and probiotics, which hold the potential for making qualitative and quantitative differences in the lives of people suffering from Crohn's," said Ghannoum.
The researchers assessed the mycobiome and bacteriome of patients with Crohn's disease and their Crohn's-free first degree relatives in nine families in northern France and Belgium, and in Crohn's-free individuals from four families living in the same geographic area.
They analysed feacal samples of 20 Crohn's and 28 Crohn's-free patients from nine families and of 21 Crohn's-free patients of four families.
The researchers found strong fungal-bacterial interactions in those with Crohn's disease: two bacteria (Escherichia coli and Serratia marcescens) and one fungus (Candida tropicalis) moved in lock step.
Test-tube research by the team found that the three work together to produce a biofilm - a thin, slimy layer of microorganisms found in the body that adheres to, among other sites, a portion of the intestines - which can prompt inflammation that results in the symptoms of Crohn's disease.
This is first time any fungus has been linked to Crohn's in humans; previously it was only found in mice with the disease, researchers said.
The finding was published in the journal mBio.
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