Gut bacterial and fungal community interactions identified for first time as a factor in Crohn’s disease


Crohn’s disease (CD) is a relapsing inflammatory bowel disease that results from a complex interplay between host genetic factors and endogenous microbial communities. Host factors and environmental factors may have effects on the microbiota and possibly initiate inflammation, but then gut dysbiosis may play a role in maintaining this cycle of inflammation.

While the vast majority of studies have focused on the gut bacterial microbiota (bacteriome), little attention has been paid to the fungal community (mycobiome).

A recent study, led by Prof. Mahmoud A. Ghannoum from the Centre for Medical Mycology at the Case Western Reserve University in Cleveland, Ohio, USA, has identified new specific interkingdom bacteria and fungi interactions that may be key players in Crohn’s disease.

The researchers assessed the bacteriome and mycobiome of patients with CD and their nondiseased first-degree relatives in 9 families in northern France and Belgium and in 4 healthy control families living in the same geographic area. Specifically, they analysed faecal samples of 20 Crohn’s and 28 Crohn’s-free individuals from the 9 families and of 21 Crohn’s-free individuals from the 4 unrelated families.

Microbial interactions leading to dysbiosis in CD have been characterized. In this study, abundance of potentially pathogenic bacteria was increased while beneficial bacteria were decreased in CD patients, which agree with past results. There was an increase in the abundance of potentially pathogenic bacterial species like Escherichia coli, Serratia marcescens, and Ruminococcus gnavus in CD patients. In contrast, the abundance of Faecalibacterium prausnitzii was reduced in CD. Regarding the mycobiome, the abundance of the non-pathogenic yeast Saccharomyces cerevisiae tended to decrease in CD patients, while Candida tropicalis abundance was significantly increased and positively correlated with levels of anti-Saccharomyces cerevisiae antibodies, which are a known CD biomarker reportedly generated by Candida.

The abundance of C. tropicalis was positively correlated with S. marcescens and E. coli, suggesting that these organisms interact in the gut. To validate these correlations, the researchers explored these interactions through in vitro biofilm formation and observed that the three organisms worked together to produce a biofilm in which S. marcescens cells interacted with both C. tropicalis and E. coli through fimbriae produced by S. marcescens cells.

On the whole, these results show that interactions between the gut bacteriome and mycobiome are closely associated with CD. The three organisms C. tropicalis, S. marescens and E. coli were highly correlated in individuals with CD and may be key determinants of CD development.



Hoarau G, Mukherjee PK, Gower-Rousseau C, et al. Bacteriome and mycobiome interactions underscore microbial dysbiosis in familiar Crohn’s disease. mBio. 2016; 7(5):e01250-16. doi: 10.1128/mBio.01250-16.

Andreu Prados
Andreu Prados
Andreu Prados holds a Bachelor of Science Degree in Pharmacy & Human Nutrition and Dietetics. Science writer specialised in gut microbiota and probiotics, working also as lecturer and consultant in nutrition and healthcare. Follow Andreu on Twitter @andreuprados