Metaproteomics reveals diet-induced changes in gut microbiome function according to Crohn's disease location

Abstract

Background: Crohn's disease (CD) is characterized by chronic intestinal inflammation. Diet is a key modifiable factor influencing the gut microbiome (GM) and a risk factor for CD. However, the impact of diet modulation on GM function in CD patients is understudied. Herein, we evaluated the effect of a high-fiber, low-fat diet (the Mi-IBD diet) on GM function in CD patients. All participants were instructed to follow the Mi-IBD diet for 8 weeks. One group of CD patients received one-time diet counseling only (Gr1); catered food was supplied for the other three groups, including CD patients (Gr2) and dyads of CD patients and healthy household controls (HHCs) residing within the same household (Gr3-HHC dyads). Stool samples were collected at baseline, week 8, and week 36, and analyzed by liquid chromatography-tandem mass spectrometry.

Results: At baseline, the metaproteomic profiles of CD patients and HHCs differed. The Mi-IBD diet significantly increased carbohydrate and iron transport and metabolism. The predicted microbial composition underlying the metaproteomic changes differed between patients with ileal only disease (ICD) or colonic involvement: ICD was characterized by decreased Faecalibacterium abundance. Even on the Mi-IBD diet, the CD patient metaproteome displayed significant underrepresentation of carbohydrate and purine/pyrimidine synthesis pathways compared to that of HHCs. Human immune-related proteins were upregulated in CD patients compared to HHCs.

Conclusions: The Mi-IBD diet changed the microbial function of CD patients and enhanced carbohydrate metabolism. Our metaproteomic results highlight functional differences in the microbiome according to disease location. Notably, our dietary intervention yielded the most benefit for CD patients with colonic involvement compared to ileal-only disease. Video Abstract.

Keywords: Crohn’s disease; Diet intervention; Functional analysis; Gut microbiota; Metaproteomics.

Fig. 1

Differences in CD phenotype according to disease location. Numbers reflect the distribution of patients in the current study

Fig. 2

Participant sample sizes and experimental flowchart. Illustration created using icons from BioRender and Noun Project

Fig. 3

Mean daily macronutrient intake. A Fiber intake, B fat intake, and C protein intake of participants in each group at the three time points (baseline, after consuming the catered food for 8 weeks, and at the end of the study period). Catered food was provided before week 8 data collection. Lighter colors reflect increased intake; darker colors reflect decreased intake

Fig. 4

Summed intensity of taxon-specific peptides identified in Crohn’s disease (CD) samples at baseline. Bars are grouped according to disease location. L1: ileal CD, L2: ileocolonic CD, L3: colonic CD. To simplify the figure, if the algorithm assigned the LCA at the species level, the corresponding genus is displayed. Colors indicate the LCA assigned to the peptide sequence

Fig. 5

Principal coordinate plots displaying data from stool samples collected at each time point. The PERMANOVA was performed on a Bray–Curtis dissimilarity matrix calculated on the LFQ intensity for each protein group (significance: p < 0.05). A CD patients categorized by sex. B All CD patients compared with all HHCs. C All participants, categorized by group. D CD patients who received the catered diet, categorized by the presence (Gr2) or absence (Gr3) of dyadic psychosocial support. E CD patients who received the catered diet, categorized by disease location (L1 = ileal only; L2/L3 = colonic involvement)

Fig. 6

Numbers of protein groups (PGs) with increased or decreased abundance according to within- and between-group comparisons. These PGs were determined by LFQ analysis and are shown with the most representative COG categories and KEGG pathways. To simplify the figure, if the algorithm assigned the LCA at the species level, the corresponding genus is displayed. Colors indicate the LCA assigned to the peptide sequence. A Within-group analysis comparing baseline and week 8 data. B Comparison of ileal CD (L1) and colonic and ileocolonic CD (L2 + L3) groups with the HHC group. C Comparisons between and within groups of patients stratified by disease location

Fig. 7

Diet-induced changes in pathways related to SCFA metabolism. Protein groups associated with pyruvate, propanoate, and butanoate (butyrate) metabolism were increased in abundance by the dietary intervention. The COG name is displayed for each enzyme reported. COG0574: phosphoenolpyruvate carboxykinase; COG0674, COG1013: pyruvate:ferredoxin oxidoreductase; COG1882: pyruvate formate lyase; COG0282: acetate kinase; COG0183: acetyl-CoA acetyltransferase; COG1250: 3-hydroxyacyl-CoA dehydrogenase; COG1053: succinate dehydrogenase; COG1979: alcohol dehydrogenase YqhD, Fe-dependent ADH family; COG1884: methylmalonyl-CoA mutase; COG1960: acyl-CoA dehydrogenase; COG1454: alcohol dehydrogenase, class IV

Fig. 8

Diet-induced changes in some protein groups from selected COGs. B baseline, W8 week 8

Fig. 9

Bar plots of changes in the abundance of protein groups associated with SCFA metabolism pathways in L1 patients and L2/L3 patients from baseline to week 8 (after consuming the catered diet). B baseline, W8 week 8