Longitudinal changes in gut microbiota in pediatric Crohn's disease (CD)

Abstract

Introduction: There is limited knowledge on changes in the gut microbiome in response to treatment, during periods of remission and relapse in CD. The aim of this study was to analyze the longitudinal variation in gut microbiome in pediatric CD from diagnosis and correlate it to clinical and environmental features. Methods: This prospective, longitudinal, cohort study was conducted at the Murdoch Children's Research Institute, Melbourne, Australia. Gut biopsies were obtained at initial diagnosis and during follow-up examinations, 6 - 18 months after diagnosis. The bacterial V2 16S gene was amplified by PCR and sequenced by Illumina MiSeq. Bioinformatics analyses were performed using MOTHUR and oligotyping. Environmental data were obtained via a questionnaire filled out by families at diagnosis. Statistics were performed using R environment and statistic package PAST3. Results: 128 CD patients and 68 controls were enrolled, from which 345 biopsies (179 ileum; 166 colonic) were used for bacterial 16S analyses. The cohort was comprised of 83 females and 123 males with an average age of 12.12 years (3.4 - 18 years). Longitudinal biopsies (n=105) were available from 53 patients 2 - 180 months from diagnosis. The five most abundant oligotype species were Bacteroides vulgatus (21.48%), Bacteroides dorei (4.38%), Faecalibacterium prausnitzii (3.25%), Prevotella copri (3.07%) and Bacteroides dorei (2.46%) in the entire cohort. PERMANOVA statistics revealed distinct microbial profiles in CD patients and controls (p= 0.0001), which differed on the basis of gender (p=0.0002), ASCA status (p=0.0168), mode of delivery (p=0.0036) and stress (p= 0.0217). We also observed a different microbial profile in the young CD group (1 - 10 years) compared to the older group (11 - 18 years) (p= 0.0218). Analyses of longitudinal biopsies revealed a distinct microbial profile between patients in remission and relapse (p=0.0038). The distinct bacterial profiles between groups observed by PERMANOVA analyses were confirmed by supervised ordination using discriminant analysis of principal components (DAPC) using the R package Adegenet 2.0.0. ANOVA analyses revealed 23 OTP species at higher abundance in the control group. The most frequent OTP species associated with CD was Veiilonella atypica. Ruminococcus torques and Bacterium YE61 were detected at a significantly higher rate in the ASCA-positive CD group (FDR<0.05). Bacteroides fragilis, Pseudoflavonifractor capillosus and Ruminococcus gnavus were significantly underrepresented in the relapsed CD group (FDR<0.05). Conclusion: Significant differences in microbial population were noted between CD patients and controls. Longitudinal analyses revealed different microbiome profiles between patients in relapse and remission.L6128913532016-11-10 <br />