Diet, gut microbiota and metabolites in paediatric Crohn’s Disease
Research type
Research Study
Full title
Gut Microbial Taxonomy and Metabolism in Paediatric Crohn’s Disease during Exclusive and Supplementary Enteral Nutrition using OMICS Technologies.
IRAS ID
141190
Contact name
Richard K Russell
Contact email
Research summary
Summary of Research
Exclusive Enteral Nutrition (EEN) is the liquid diet given to children with active Crohn's Disease (CD). We have previously shown that EEN induces changes in major bacterial metabolites and dominant bacterial species which are more profound in children that clinically improve. We aim to determine whether it is possible to maintain these bacterial changes with prolonged supplementary enteral nutrition (SEN) while returning to normal diet and if this can reduce risk of subsequent relapse for children with CD.
New technologies will allow us to measure a broad range of bacteria and metabolites, to test if the clinical response to EEN and changes in gut inflammation are associated with bacterial composition and chemical products; and if maintenance of changes using SEN reduces the risk of relapse over a 12 month period.
We will aim to recruit all potential Crohn’s disease children coming to Yorkhill for colonoscopy. Once consented, we will ask for an initial blood, urine, faecal sample and 8 mucosal biopsies during the routine endoscopy session. If diagnosed with CD, and if their clinician prescribes treatment with EEN we will request additional blood at the end of EEN, and 5 faecal and urine samples spread over 12 months; as well as some dietary information from them.We will collect samples from up to 42 children with CD and 42 age and sex matched healthy volunteers. Initial samples taken from children who were not diagnosed with CD will be compared with CD samples to look for potential metabolic disease markers.
Characterisation of faecal bacteria and metabolites in both faeces and urine; as well as measurement of blood inflammatory biomarkers will be carried out at the University of Glasgow, Human Nutrition Section labs at Glasgow Royal infirmary and other University of Glasgow research labs as required.Summary of Results
Crohn’s disease (CD) and ulcerative colitis (UC) are the two major types of inflammatory bowel disease (IBD). Approximately 10% of patients with CD are diagnosed during adolescence or early adulthood. Several hypothesises have been proposed to explain the rising incidence in CD worldwide. In particular, the increasing use of food additives in food industrialisation has been the subject of intensive research. Results from these studies have quickly been translated to dietary recommendations and exclusions.The importance of nutrition in patients with CD has been described in several aspects of the disease, from aetiology, management, and the long-term health outcomes of the patient. Nutritional therapy in the form of exclusive enteral nutrition (EEN), is the first line treatment for the induction of remission for active disease in paediatric CD patients throughout Europe, Australia, and parts of North America. Exclusive enteral nutrition is effective in inducing clinical remission and has the additional benefit of restoring nutritional deficiencies.
Faecal calprotectin (FC) is currently the leading non-invasive biomarker of intestinal inflammation and mucosal healing. Exclusive enteral nutrition has been shown to effectively reduce the levels of FC during the course of treatment. It has also been shown that levels of FC revert to pre-treatment levels within the first four months of return to habitual diet post EEN completion. However, it is unknown how rapid this increase in FC occurs; and the extent to which maintenance therapies may be able to delay the rise.
Despite its first use in the 1970’s, the precise mechanisms of action of EEN remain elusive. Recent evidence has implicated the role of the intestinal microbiome. Exclusive enteral nutrition has been shown to lead to the reduction in concentration of certain short chain fatty acids (SCFA), to which numerous studies have attributed anti-inflammatory properties. Exclusive enteral nutrition has also been shown to increase faecal total sulphide concentrations and decrease faecal pH from acidic levels to alkaline. These counterintuitive findings have also been demonstrated with reductions in specific bacterial species, including Faecalibacterium prausnitzii, a major butyrate producer which has been suggested as a protective species in CD. As with changes in FC, many of the microbial and metabolic changes observed during EEN have been shown to revert to pre-treatment levels within the first four months of food reintroduction.
It was the aim during this study to investigate how changes that occur in the faecal microbiome and metabolome during EEN are maintained as patients return to their habitual diet. During this study the researcher recruited a cohort of paediatric CD patients with active disease prior to starting a course of EEN. Up to five stool samples were collected from each of these patients. An initial stool sample was collected from patients prior to starting EEN; two further stool samples were collected during EEN (33d & 54d EEN); and finally, two stool samples were collected during food reintroduction, the first within two weeks, and the second within two months of food reintroduction.
This study shows that FC is significantly reduced during EEN but within only 17d food reintroduction, FC levels have increased to almost baseline levels. The results from this study have also shown that patients consuming maintenance enteral nutrition (MEN) had a lower concentration of FC during the first 17d of food reintroduction than patients not using MEN. This benefit was not maintained in the longer-term phase of food reintroduction, and FC had reverted to pre-treatment levels within two months of food reintroduction.
The current study also describes changes in the faecal microbiome and metabolome from baseline, during EEN and subsequent food reintroduction. Comparisons between the faecal microbiome and metabolome of patients with CD were also made against a cohort of healthy children, patients with UC, and participants who underwent an exploratory colonoscopy for the diagnosis of IBD but after investigation did not have an IBD diagnosis. The faecal microbiome was assessed with molecular microbiology techniques through amplification of the 16s rRNA gene, and the faecal metabolome was characterised using several techniques including gas-chromatography and 1H nuclear magnetic resonance. Patients with CD had reduced species diversity and richness compared with healthy participants. During EEN this reduced diversity, relative to healthy controls, was maintained but had not changed from baseline levels. When β-diversity was assessed using Bray-Curtis dissimilarity matrix, the community structure was shown to be driven further from its position at baseline, and in the opposite direction from the HC. However, when this analysis was repeated using the unweighted UniFrac distance measure, while distinct from HC at baseline, the faecal microbiome moved to be more similar with HC by the end of EEN. During food reintroduction there was no change in β-diversity from the position at the end of EEN, when assessed using the unweighted or weighted UniFrac. However, a significant shift in β-diversity was observed during food reintroduction when β-diversity was assessed using Bray-Curtis dissimilarity.
During EEN and food reintroduction several taxa changed significantly in relative abundance. Several of the same bacterial taxa were highlighted for their importance when using advanced bioinformatic techniques including sparse projection to latent structure – discriminant analysis (sPLS-DA), random forest modelling and during correlation analysis with FC. More specifically, these analyses repeatedly implicated genera from Faecalibacterium, Haemophilus, and Veillonella as important in driving changes in the faecal microbiome community structure and correlating significantly with absolute concentrations of FC.
This study has confirmed the earlier evidence of the significant reduction in FC during EEN, which is paralleled with reduction in SCFAs, faecal pH and increased faecal total sulphide. As FC increases rapidly within 17d of food reintroduction, current disease maintenance strategies are inadequate at preventing the development of subclinical inflammation. Future research should explore dietary triggers of CD relapse during the food-reintroduction phase and their interplay with the gut microbiome and metabolome.
REC name
West of Scotland REC 5
REC reference
14/WS/1004
Date of REC Opinion
24 Jun 2014
REC opinion
Favourable Opinion