Observational Study
Copyright ©The Author(s) 2018. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. Oct 21, 2018; 24(39): 4510-4516
Published online Oct 21, 2018. doi: 10.3748/wjg.v24.i39.4510
Fungal dysbiosis predicts the diagnosis of pediatric Crohn’s disease
Mohammad I El Mouzan, Kirill S Korolev, Mohammad A Al Mofarreh, Rajita Menon, Harland S Winter, Ahmad A Al Sarkhy, Scot E Dowd, Ahmad M Al Barrag, Asaad A Assiri
Mohammad I El Mouzan, Ahmad A Al Sarkhy, Department of Pediatrics, King Saud University, Riyadh 11461, Saudi Arabia
Kirill S Korolev, Rajita Menon, Bioinformatics Program, Boston University, Boston, MA 02215, United States
Mohammad A Al Mofarreh, Al Mofarreh PolyClinic, Riyadh 11423, Saudi Arabia
Harland S Winter, MassGeneral Hospital for Children, Boston, MA 02114, United States
Scot E Dowd, MRDNA, Shallowater, TX 79363, United States
Ahmad M Al Barrag, Department of Microbiology, King Saud University, Riyadh 11461, Saudi Arabia
Asaad A Assiri, Department of Pediatrics, Supervisor of Prince Abdullah Bin Khalid Celiac Disease Research Chair, King Saud University, Riyadh 11461, Saudi Arabia
Author contributions: El Mouzan MI and Winter HS contributed to the conception and design of the study; Al Mofarreh MA, Al Sarkhy AA, Assiri AA and Al Barrag AM contributed to data acquisition and samples’ storage; Dowd SE performed DNA extraction and fungal sequencing; Korolev KS and Menon R performed the biostatistics and bioinformatics; El Mouzan MI drafted the manuscript and all co-authors contributed to reviewing, editing and giving approval of the final manuscript.
Institutional review board statement: The manuscript is part of the study of the characteristics of inflammatory bowel disease in Saudi children approved by the IRB of the College of Medicine, King Saud University (No: 10/2647/IRB dated 29/6/2010).
Informed consent statement: Parents and/or children gave consent and/or assent to participate in the study before enrollment.
Conflict-of-interest statement: All authors declare no conflict of interest related to this study.
STROBE statement: The authors have read the STROBE Statement-checklist of items, and the manuscript was prepared and revised according to the STROBE Statement - checklist items
Open-Access: This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/
Correspondence to: Mohammad I El Mouzan, MD, Professor and Consultant Pediatrician, Department of Pediatrics, Gastroenterology Unit, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia. drmouzan@gmail.com
Telephone: +966-55-5479281 Fax: +966-11-4679364
Received: June 29, 2018
Peer-review started: July 2, 2018
First decision: July 12, 2018
Revised: September 3, 2018
Accepted: October 5, 2018
Article in press: October 5, 2018
Published online: October 21, 2018

To investigate the accuracy of fungal dysbiosis in mucosa and stool for predicting the diagnosis of Crohn’s disease (CD).


Children were prospectively enrolled in two medical centers: one university hospital and one private gastroenterology clinic in the city of Riyadh, Kingdom of Saudi Arabia. The children with confirmed diagnosis of CD by standard guidelines were considered cases, and the others were considered non-inflammatory bowel disease controls. Mucosal and stool samples were sequenced utilizing Illumina MiSeq chemistry following the manufacturer’s protocols, and abundance and diversity of fungal taxa in mucosa and stool were analyzed. Sparse logistic regression was used to predict the diagnosis of CD. The accuracy of the classifier was tested by computing the receiver operating characteristic curves with 5-fold stratified cross-validation under 100 permutations of the training data partition and the mean area under the curve (AUC) was calculated.


All the children were Saudi nationals. There were 15 children with CD and 20 controls. The mean age was 13.9 (range: 6.7-17.8) years for CD children and 13.9 (3.25-18.6) years for controls, and 10/15 (67%) of the CD and 13/20 (65%) of the control subjects were boys. CD locations at diagnosis were ileal (L1) in 4 and colonic (L3) in 11 children, while CD behavior was non-stricturing and non-penetrating (B1) in 12 and stricturing (B2) in 3 children. The mean AUC for the fungal dysbiosis classifier was significantly higher in stools (AUC = 0.85 ± 0.057) than in mucosa (AUC = 0.71 ± 0.067) (P < 0.001). Most fungal species were significantly more depleted in stools than mucosal samples, except for Saccharomyces cerevisiae and S. bayanus, which were significantly more abundant. Diversity was significantly more reduced in stools than in mucosa.


We found high AUC of fungal dysbiosis in fecal samples of children with CD, suggesting high accuracy in predicting diagnosis of CD.

Keywords: Fungiome, Mycobiome, Crohn’s disease, Inflammation, Saudi children

Core tip: We found high accuracy of fungal dysbiosis in predicting diagnosis of Crohn’s disease (CD), a finding similar to bacterial dysbiosis. However, the higher area under the curve for the fungal dysbiosis classifier in stool (0.85 ± 0.057) than in mucosa (0.71 ± 0.067) (P < 0.001), contrasts with bacterial studies, suggesting higher accuracy of stool samples. Although the clinical application of this finding is limited at present by the high cost of fungal analysis, such information is important from a scientific viewpoint, to increase the understanding of the role of fungal flora in CD and to stimulate further studies.