Basic Study
Copyright ©The Author(s) 2019. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. May 14, 2019; 25(18): 2204-2216
Published online May 14, 2019. doi: 10.3748/wjg.v25.i18.2204
Characteristics of mucosa-associated gut microbiota during treatment in Crohn’s disease
Cong He, Huan Wang, Wang-Di Liao, Chao Peng, Xu Shu, Xuan Zhu, Zhen-Hua Zhu
Cong He, Huan Wang, Wang-Di Liao, Chao Peng, Xu Shu, Xuan Zhu, Zhen-Hua Zhu, Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
Author contributions: He C, Wang H and Liao WD contributed to equally to this work; He C and Zhu ZH designed the research; Wang H, Liao WD, Peng C, Shu X and Zhu X enrolled the qualified patients and collected the mucosal samples; Wang H analyzed the information of the patients during treatment; He C performed the bioinformatic analysis and wrote the paper; all authors have read and approved the final version to be published.
Supported by: the National Natural Science Foundation of China, No. 81660101 and No. 81860106; the Special Scientific Research Fund of Public Welfare Profession of National Health and Family Planning Commission, No. 201502026; and the Graduate Innovation Fund of Nanchang University, No. CX2017251.
Institutional review board statement: The study was reviewed and approved by the Medical Ethics Committee of Nanfang Hospital. All routine colonic biopsy specimens from the patients were taken after informed consent and ethical permission was obtained for participation in the study.
Conflict-of-interest statement: To the best of our knowledge, no conflict of interest exists.
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:
Corresponding author: Zhen-Hua Zhu, PhD, Doctor, Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, 17 Yong Waizheng Street, Donghu District, Nanchang 330006, Jiangxi Province, China.
Telephone: +86-791-88692705 Fax: +86-791-88623153
Received: January 6, 2019
Peer-review started: January 7, 2019
First decision: March 13, 2019
Revised: March 25, 2019
Accepted: April 10, 2019
Article in press: April 10, 2019
Published online: May 14, 2019

The dysbiosis of the gut microbiome is evident in Crohn’s disease (CD) compared with healthy controls (HC), although the alterations from active CD to remission after treatment are unclear.


To characterize the mucosa-associated gut microbiota in patients with CD before and after the induction therapy.


The basic information was collected from the subjects and the CD activity index (CDAI) was calculated in patients. A 16S rRNA sequencing approach was applied to determine the structures of microbial communities in mucosal samples including the terminal ileal, ascending colon, descending colon and rectum. The composition and function of mucosa-associated gut microbiota were compared between samples from the same cohort of patients before and after treatment. Differential taxa were identified to calculate the microbial dysbiosis index (MDI) and the correlation between MDI and CDAI was analyzed using Pearson correlation test. Predictive functional profiling of microbial communities was obtained with PICRUSt.


There were no significant differences in microbial richness among the four anatomical sites in individuals. Compared to active disease, the alpha diversity of CD in remission was increased towards the level of HC compared to the active stage. The principal coordinate analysis revealed that samples of active CD were clearly separated from those in remission, which clustered close to HC. Sixty-five genera were identified as differentially abundant between active and quiescent CD, with a loss of Fusobacterium and a gain of potential beneficial bacteria including Lactobacillus, Akkermansia, Roseburia, Ruminococcus and Lachnospira after the induction of remission. The combination of these taxa into a MDI showed a positive correlation with clinical disease severity and a negative correlation with species richness. The increased capacity for the inferred pathways including Lipopolysaccharide biosynthesis and Lipopolysaccharide biosynthesis proteins in patients before treatment negatively correlated with the abundance of Roseburia, Ruminococcus and Lachnospira.


The dysbiosis of mucosa-associated microbiota was associated with the disease phenotype and may become a potential diagnostic tool for the recurrence of disease.

Keywords: Crohn’s disease, Mucosa-associated gut microbiota, Active, Remission, 16S rRNA sequence

Core tip: The dysbiosis of gut microbiome is associated with the development of Crohn’s disease (CD), although the alteration from active CD to remission after treatment is unclear. This study illustrated that the composition of mucosa-associated gut microbiota in active CD significantly changed after the induction of remission regardless of drugs used, which got close to healthy subjects. We speculate that the maintenance of gut microbiota balance may be potential therapeutic target for reducing the risk of disease relapse.