Variability of core microbiota in newly diagnosed treatment-naive paediatric inflammatory bowel disease patients

T. G. J. de Meij; E. F. J. de Groot; C. F. W. Peeters; N. K. H. de Boer; C. M. F. Kneepkens; A. Eck; M. A. Benninga; P. H. M. Savelkoul; A. A. van Bodegraven; A. E. Budding

doi:10.1371/journal.pone.0197649

Variability of core microbiota in newly diagnosed treatment-naive paediatric inflammatory bowel disease patients

T. G. J. de Meij^*, E. F. J. de Groot, C. F. W. Peeters, N. K. H. de Boer, C. M. F. Kneepkens, A. Eck, M. A. Benninga, P. H. M. Savelkoul, A. A. van Bodegraven, A. E. Budding

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Background & aims

Intestinal microbiota is considered to play a crucial role in the aetiology of inflammatory bowel disease (IBD). We aimed to describe faecal microbiota composition and dynamics in a large cohort of children with de novo (naive) IBD, in comparison to healthy paediatric controls (HC).

Methods

In this prospective study, performed at two tertiary centres, faecal samples from newly diagnosed, treatment-naive paediatric IBD patients were collected prior to bowel cleansing for colonoscopy (t0) and 1, 3 and 6 weeks and 3 months after initiation of therapy. The microbial profiles of Crohn's disease (CD) and Ulcerative colitis (UC) patients were compared with HC and linked to therapeutic response. Microbiota composition was analysed by IS-pro technology.

Results

Microbial profiles of 104 new IBD-patients (63 CD, 41 UC, median age 14.0 years) were compared to 61 HC (median 7.8 years). IBD was mainly characterised by decreased abundance of Alistipes finegoldii and Alistipes putredinis, which characterize a healthy state microbial core. The classifier including these core species as predictors achieved an AUC of the ROC curve of .87. Core bacteria tended to regain abundance during treatment, but did not reach healthy levels.

Conclusion

Faecal microbiota profiles of children with de novo CD and UC can be discriminated from HC with high accuracy, mainly driven by a decreased abundance of species shaping the microbial core in the healthy state. Paediatric IBD can therefore be characterized by decreased abundance of certain bacterial species reflecting the healthy state rather than by the introduction of pathogens.

Original language	English
Article number	0197649
Number of pages	20
Journal	PLOS ONE
Volume	13
Issue number	8
DOIs	https://doi.org/10.1371/journal.pone.0197649
Publication status	Published - 13 Aug 2018

Keywords

CROHNS-DISEASE
GUT MICROBIOTA
INTESTINAL MICROBIOTA
ENTERAL NUTRITION
FECAL MICROBIOTA
RISING INCIDENCE
CHILDREN
PATHOGENESIS
IMPROVEMENT
MODULATION

Access to Document

10.1371/journal.pone.0197649Licence: CC BY

Cite this

de Meij, T. G. J., de Groot, E. F. J., Peeters, C. F. W., de Boer, N. K. H., Kneepkens, C. M. F., Eck, A., Benninga, M. A., Savelkoul, P. H. M., van Bodegraven, A. A., & Budding, A. E. (2018). Variability of core microbiota in newly diagnosed treatment-naive paediatric inflammatory bowel disease patients. PLOS ONE, 13(8), Article 0197649. https://doi.org/10.1371/journal.pone.0197649

@article{39594645ee7a4a73a57219e3cbf69ba2,

title = "Variability of core microbiota in newly diagnosed treatment-naive paediatric inflammatory bowel disease patients",

abstract = "Background & aimsIntestinal microbiota is considered to play a crucial role in the aetiology of inflammatory bowel disease (IBD). We aimed to describe faecal microbiota composition and dynamics in a large cohort of children with de novo (naive) IBD, in comparison to healthy paediatric controls (HC).MethodsIn this prospective study, performed at two tertiary centres, faecal samples from newly diagnosed, treatment-naive paediatric IBD patients were collected prior to bowel cleansing for colonoscopy (t0) and 1, 3 and 6 weeks and 3 months after initiation of therapy. The microbial profiles of Crohn's disease (CD) and Ulcerative colitis (UC) patients were compared with HC and linked to therapeutic response. Microbiota composition was analysed by IS-pro technology.ResultsMicrobial profiles of 104 new IBD-patients (63 CD, 41 UC, median age 14.0 years) were compared to 61 HC (median 7.8 years). IBD was mainly characterised by decreased abundance of Alistipes finegoldii and Alistipes putredinis, which characterize a healthy state microbial core. The classifier including these core species as predictors achieved an AUC of the ROC curve of .87. Core bacteria tended to regain abundance during treatment, but did not reach healthy levels.ConclusionFaecal microbiota profiles of children with de novo CD and UC can be discriminated from HC with high accuracy, mainly driven by a decreased abundance of species shaping the microbial core in the healthy state. Paediatric IBD can therefore be characterized by decreased abundance of certain bacterial species reflecting the healthy state rather than by the introduction of pathogens.",

keywords = "CROHNS-DISEASE, GUT MICROBIOTA, INTESTINAL MICROBIOTA, ENTERAL NUTRITION, FECAL MICROBIOTA, RISING INCIDENCE, CHILDREN, PATHOGENESIS, IMPROVEMENT, MODULATION",

author = "{de Meij}, {T. G. J.} and {de Groot}, {E. F. J.} and Peeters, {C. F. W.} and {de Boer}, {N. K. H.} and Kneepkens, {C. M. F.} and A. Eck and Benninga, {M. A.} and Savelkoul, {P. H. M.} and {van Bodegraven}, {A. A.} and Budding, {A. E.}",

year = "2018",

month = aug,

day = "13",

doi = "10.1371/journal.pone.0197649",

language = "English",

volume = "13",

journal = "PLOS ONE",

issn = "1932-6203",

publisher = "Public Library of Science",

number = "8",

}

TY - JOUR

T1 - Variability of core microbiota in newly diagnosed treatment-naive paediatric inflammatory bowel disease patients

AU - de Meij, T. G. J.

AU - de Groot, E. F. J.

AU - Peeters, C. F. W.

AU - de Boer, N. K. H.

AU - Kneepkens, C. M. F.

AU - Eck, A.

AU - Benninga, M. A.

AU - Savelkoul, P. H. M.

AU - van Bodegraven, A. A.

AU - Budding, A. E.

PY - 2018/8/13

Y1 - 2018/8/13

N2 - Background & aimsIntestinal microbiota is considered to play a crucial role in the aetiology of inflammatory bowel disease (IBD). We aimed to describe faecal microbiota composition and dynamics in a large cohort of children with de novo (naive) IBD, in comparison to healthy paediatric controls (HC).MethodsIn this prospective study, performed at two tertiary centres, faecal samples from newly diagnosed, treatment-naive paediatric IBD patients were collected prior to bowel cleansing for colonoscopy (t0) and 1, 3 and 6 weeks and 3 months after initiation of therapy. The microbial profiles of Crohn's disease (CD) and Ulcerative colitis (UC) patients were compared with HC and linked to therapeutic response. Microbiota composition was analysed by IS-pro technology.ResultsMicrobial profiles of 104 new IBD-patients (63 CD, 41 UC, median age 14.0 years) were compared to 61 HC (median 7.8 years). IBD was mainly characterised by decreased abundance of Alistipes finegoldii and Alistipes putredinis, which characterize a healthy state microbial core. The classifier including these core species as predictors achieved an AUC of the ROC curve of .87. Core bacteria tended to regain abundance during treatment, but did not reach healthy levels.ConclusionFaecal microbiota profiles of children with de novo CD and UC can be discriminated from HC with high accuracy, mainly driven by a decreased abundance of species shaping the microbial core in the healthy state. Paediatric IBD can therefore be characterized by decreased abundance of certain bacterial species reflecting the healthy state rather than by the introduction of pathogens.

AB - Background & aimsIntestinal microbiota is considered to play a crucial role in the aetiology of inflammatory bowel disease (IBD). We aimed to describe faecal microbiota composition and dynamics in a large cohort of children with de novo (naive) IBD, in comparison to healthy paediatric controls (HC).MethodsIn this prospective study, performed at two tertiary centres, faecal samples from newly diagnosed, treatment-naive paediatric IBD patients were collected prior to bowel cleansing for colonoscopy (t0) and 1, 3 and 6 weeks and 3 months after initiation of therapy. The microbial profiles of Crohn's disease (CD) and Ulcerative colitis (UC) patients were compared with HC and linked to therapeutic response. Microbiota composition was analysed by IS-pro technology.ResultsMicrobial profiles of 104 new IBD-patients (63 CD, 41 UC, median age 14.0 years) were compared to 61 HC (median 7.8 years). IBD was mainly characterised by decreased abundance of Alistipes finegoldii and Alistipes putredinis, which characterize a healthy state microbial core. The classifier including these core species as predictors achieved an AUC of the ROC curve of .87. Core bacteria tended to regain abundance during treatment, but did not reach healthy levels.ConclusionFaecal microbiota profiles of children with de novo CD and UC can be discriminated from HC with high accuracy, mainly driven by a decreased abundance of species shaping the microbial core in the healthy state. Paediatric IBD can therefore be characterized by decreased abundance of certain bacterial species reflecting the healthy state rather than by the introduction of pathogens.

KW - CROHNS-DISEASE

KW - GUT MICROBIOTA

KW - INTESTINAL MICROBIOTA

KW - ENTERAL NUTRITION

KW - FECAL MICROBIOTA

KW - RISING INCIDENCE

KW - CHILDREN

KW - PATHOGENESIS

KW - IMPROVEMENT

KW - MODULATION

U2 - 10.1371/journal.pone.0197649

DO - 10.1371/journal.pone.0197649

M3 - Article

SN - 1932-6203

VL - 13

JO - PLOS ONE

JF - PLOS ONE

IS - 8

M1 - 0197649

ER -