This study identified differences in the intake of certain nutrients, dietary patterns, and diet-related biomarkers in faeces between children with CD who demonstrated different levels of intestinal inflammation after food reintroduction, following successful treatment with EEN.
A higher intake of fibre and of butyrate, its proxy biomarker in faeces, was observed in patients with raised levels of FC. This observation is in contrast to the previously ascribed protective role of fibre in the development of CD(3, 24, 25), but aligns with the lack of evidence supporting the effectiveness of fibre in the management of the disease (26–28). A compositional analysis of 61 EEN formulas used for the induction of remission in CD also showed that < 20% of those formulas contained fibre(29). Collectively, these results demonstrate that lack of fibre does not have a deleterious effect on disease activity, and indeed may have a seemingly unexpected unfavourable effect.
Patients in the current study with higher FC levels reported a higher protein and phosphorus intake, along with a higher intake of red and processed meat. High intake of animal protein has been associated with development of IBD(30, 31), and in patients with ulcerative colitis (UC), high intake of protein, total, as well as red and processed meat, was positively associated with risk of relapse(15). In contrast, a recent RCT showed that clinical relapse rates and FC levels did not differ between patients with CD who consumed at least two portions of red and processed meat per week, and others who consumed less than one serving per month(32). The positive associations between FC and phosphorus intake may indicate an increased intake of grains and meat products which are rich in phosphorus. Although the effect of phosphorus has not been extensively explored in human IBD, dietary phosphate has been shown to be pro-inflammatory in animals(33).
Using machine learning on food group-based analysis, we showed that a dietary pattern consisting of cereal and meat-based products could successfully predict the assignment of 92% of patients into their respective FC group. In a recent cross-sectional study of patients with CD, principal component analysis also identified that a dietary pattern rich in rice, pasta and red meat, among other foods, was associated with increased symptom frequency, but did not differentiate patients with active disease from those in remission(34). In the current study, patients with higher FC levels also reported a higher consumption of gluten containing cereal products, which points to gluten-containing foods as potential driver of intestinal inflammation.
In addition to conventional dietary assessment, we measured diet-originating bacterial metabolites and dietary components in faeces as complementary biomarkers of consumption of certain foods previously implicated in CD pathogenesis(35). The lack of significant differences in the levels of faecal starch between the two CD groups did not parallel the signals we observed with fibre intake. However, fibre encompasses an umbrella term of structurally diverse carbohydrates with potentially different roles in CD(36). Although the intake of gluten containing cereals was higher in Group A, faecal GIP levels did not differ between the two groups. However, the method used to quantify faecal GIP is sensitive at detecting transgressions to gluten-free diet compliance rather than quantitatively estimating variable intakes of gluten, which might be more important in a dose-response relationship with initiation of intestinal inflammation(19).
In the current study, double levels of faecal butyrate levels were observed in patients with higher FC levels after food reintroduction. This signal was associated with higher dietary fibre intake from which butyrate originates as an end-product of bacterial fermentation in the same group (Spearman’s correlation between fibre and butyrate levels: rho = 0.55, p = 0.051)(37). Higher levels of butyrate in the caecum have been shown to aggravate animal colitis(36) and a significant reduction in butyrate levels in faecal samples of children responding to EEN paralleled with a decrease in FC(18, 38). These data suggest that high amounts of butyrate are not of crucial importance for maintenance of intestinal health in patients with CD and its role in the disease course requires further exploration.
Although patients in Group A reported higher protein intakes compared to those in Group B, there were no significant differences in BCFA levels between the two groups. This could potentially result from adequate intake of dietary fibre in those patients, hence exceeding the threshold below which excessive protein fermentation occurs in the colon.
The small sample size is the main limitation of this pilot study. This was due to the modest number of patients who met our stringent inclusion criteria and few patients who did not return dietary records paired with faecal samples. However, selection of a homogenous population with all patients enrolled at the end of an EEN course and while they were still in clinical remission, without receiving other concomitant induction treatment, minimised variance in our measured outcomes and increased statistical power. Beyond the dietary analysis presented here, the observed dietary signals of the current study might also represent biomarkers of unidentified covariates of other food ingredients which might be important in gut inflammation in CD. An indicative example could be baker’s yeast, which is present in bread and bakery products, constitutes a significant proportion of the cereal and cereal-based products group, and has been previously implicated in aggravating disease activity in CD(39). It is also possible that nutrient interactions are more important than single nutrients alone in the underlying pathogenesis of CD(40). Measurement of SCFA in faeces is the abstract of net production and absorption. However, as direct measurement of SCFA in the caecum would be almost impossible, faecal SCFA are considered suitable proxies of intestinal SCFA production; and by extension of fibre intake as has been demonstrated here by the positive associations between the amount of fibre consumed and levels of faecal SCFA(41, 42).