A diversified dietary pattern is associated with a balanced gut microbial composition of Faecalibacterium and Escherichia/Shigella in patients with Crohn's disease in remission

BACKGROUND AND AIMS: Crohn's disease (CD) is associated with alterations in gut microbial composition and function. This controlled-intervention study investigated the relationship between patterns of dietary intake and baseline gut microbiota in CD patients in remission and examined the effects of a dietary intervention in patients consuming a non-diversified diet (NDD).

METHODS: Forty outpatients with quiescent CD were recruited in Calgary, Alberta Canada. Based on 3-day food records, patients consuming a lower plant-based and higher red and processed meat-based diet were assigned to the NDD group (n=15) and received a 12-week structured dietary intervention; all other patients were assigned to the diversified diet (DD) control group (n=25) and received conventional management. Fecal microbiota composition, short chain fatty acids (SCFAs) and calprotectin were measured.

RESULTS: At baseline NDD and DD groups had a different fecal microbial beta-diversity (p=0.003, PERMANOVA). NDD group had lower Faecalibacterium and higher Escherichia/Shigella relative abundances compared to the DD group (3.3±5.4% vs. 8.5±10.6%; 6.9±12.2% vs. 1.6±4.4%; p≤0.03, ANCOVA). These two genera showed a strong negative correlation (rs= -0.60, q=0.0002). Fecal butyrate demonstrated a positive correlation with Faecalibacterium (rs=0.52, q=0.002), and an inhibitory relationship with Escherichia/Shigella abundance (four-parameter sigmoidal model, R= -0.83; rs= -0.44, q=0.01), respectively. After the 12 weeks dietary intervention, no difference in microbial beta-diversity between the two groups was observed (p=0.43). The NDD group demonstrated an increase in Faecalibacterium (p<0.05, GEE), and resembled the DD group at the end of the intervention (p=0.84, t-test with permutation). We did not find association of diet with fecal SCFAs or calprotectin.

CONCLUSIONS: Dietary patterns are associated with specific gut microbial compositions in CD patients in remission. A diet intervention in patients consuming a NDD modifies gut microbial composition to resemble that seen in patients consuming a DD. These results identify that diet is important in shaping the microbial dysbiosis signature in CD towards a balanced community.