Reversion To Baseline Microbiome Following Successful Course Of Exclusive Enteral Nutrition In Paediatric Crohn'S Disease

IntroductionTo characterise the microbiome composition and functionality in paediatric Crohn’s disease (CD) patients during a course of exclusive enteral nutrition (EEN) and subsequent food-reintroductionMethodsCD patients were recruited between August 2014-June 2016. Patients were treated with an 8 wk course of EEN. Clinical disease activity was defined using the weighted paediatric Crohn’s disease activity index (wPCDAI). Serial faecal samples were collected prior to EEN, at 30d and 56d of EEN, and two further samples were collected post-EEN (17d and 52d) during food re-introduction (FR). Microbiome was assessed by 16s rRNA gene sequencing of the V4 region performed on the MiSeq (Illumina). Community structure was resolved at 97% similarity operational taxonomic unit (OTU). Short chain fatty acids (SCFA) were quantified with gas chromatography and are expressed in µmol/g. Faecal calprotectin (FC) was measured using the CALPROLAB0170 (ALP) (Lysaker, Norway) ELISA kit. Continuous data are present as mean and standard deviation unless otherwise stated.Results66 CD patients were recruited (Female 25; age 13.4 yr). Clinical remission (wPCDAI<12.5) was achieved in 41 (62%). During EEN there was an increase in Shannon diversity (start: 0.3 [0.22] vs 30d EEN: 0.48 [0.2], p<0.001; vs 56d EEN: 0.43 [0.27], p=0.05). During FR these indices did not change. Based on β-diversity dispersion analysis, estimated using Bray-Curtis distance, EEN induced clear alterations to the microbiome. Permutation ANOVA was used to identify significant changes to the microbiome during EEN. Most of the change that occurred was apparent within the first 4 weeks of treatment with R2: 4.7%, (p=0.001) and by the end of EEN R2: 3.2%, (p=0.001). In patients to enter remission using EEN, we observed a quick reversion in the microbiome composition to that of pretreatment (p=0.23). Assessing the metabolic activity of the microbiome we observed a significant decrease in the concentration of acetate (start: 423.6 [183.6], end: 224.9 [101.5]; p< 0.001), propionate (start: 93.8 [50.6], end: 55.7 [27.3]; p< 0.001) and butyrate (start: 95.0 [64.2], end: 41.0 [50.7]; p< 0.001). During FR, there was a rapid reversion in levels of acetate and propionate (acetate EEN end: 224.9 [101.5] vs 17d FR: 362.4 [179.7]; p=0.003; propionate EEN end: 55.7 [27.3] vs 17d FR: 93.0 [46.9]; p=0.002). Faecal calprotectin significantly decreased during EEN (start: 1402.4 [586.3]; 4wk EEN: 877.5 [593.1], p<0.001; 8wk EEN: 720 [664], p<0.001) and was quickly reversed during food re-introduction (17d FR: 1025 [603], p=0.025; 52d FR: 1105 [651], p=0.003)ConclusionsEEN induces specific effects on faecal microbiome and markers of functional activity. This is characterised by a reduction in metabolic activity during EEN, with reversion to pre-EEN state during food re-introduction paralleling an elevation of faecal calprotectin