Dutta AK, Abraham D, Praharaj I, Benny B, Govindan K, Zondervenni Z, Joseph A. Dynamics of tissue and fecal microbiota in active Crohn’s disease and their ability to predict disease state. World J Gastrointest Pathophysiol 2025; 16(3): 108058 [PMID: 41024987 DOI: 10.4291/wjgp.v16.i3.108058]
Corresponding Author of This Article
Amit K Dutta, Academic Fellow, Professor, Department of Gastroenterology, Christian Medical College, Ida Scudder Road, Vellore 632004, Tamil Nadu, India. akdutta1995@gmail.com
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Gastroenterology & Hepatology
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Observational Study
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Sep 22, 2025 (publication date) through Feb 18, 2026
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World Journal of Gastrointestinal Pathophysiology
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2150-5330
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Dutta AK, Abraham D, Praharaj I, Benny B, Govindan K, Zondervenni Z, Joseph A. Dynamics of tissue and fecal microbiota in active Crohn’s disease and their ability to predict disease state. World J Gastrointest Pathophysiol 2025; 16(3): 108058 [PMID: 41024987 DOI: 10.4291/wjgp.v16.i3.108058]
World J Gastrointest Pathophysiol. Sep 22, 2025; 16(3): 108058 Published online Sep 22, 2025. doi: 10.4291/wjgp.v16.i3.108058
Dynamics of tissue and fecal microbiota in active Crohn’s disease and their ability to predict disease state
Amit K Dutta, Dilip Abraham, Ira Praharaj, Blossom Benny, Karthikeyan Govindan, Zayina Zondervenni, AJ Joseph
Amit K Dutta, AJ Joseph, Department of Gastroenterology, Christian Medical College, Vellore 632004, Tamil Nadu, India
Dilip Abraham, Blossom Benny, Karthikeyan Govindan, Zayina Zondervenni, Wellcome Trust Research Laboratory, Christian Medical College Vellore, Vellore 632004, Tamil Nadu, India
Ira Praharaj, Regional Medical Research Centre, Indian Council of Medical Research Regional Medical Research Centre Bhubaneswar, Bhubaneshwar 751023, Odisha, India
Author contributions: Dutta AK, Abraham D, Praharaj I, Benny B, Govindan K, Zondervenni Z, and Joseph AJ carried out the research, collection and interpretation of the data; Dutta AK carried out the planning; Dutta AK and Abraham D drafted the manuscript; Praharaj I, Benny B, Govindan K, Zondervenni Z, and Joseph AJ made important revisions to the manuscript; and all authors have read and approved the final manuscript.
Supported by the Science and Engineering Research Board, No. EMR/2016/007033.
Institutional review board statement: This study was approved by the Medical Ethics Committee of Christian Medical College Vellore, approval No. 10698.
Informed consent statement: Written informed consent was obtained from all the participants before enrolment into this study.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
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 of items.
Data sharing statement: The microbiome sequencing data from this study will be made available for research purpose on request to the corresponding author.
Corresponding author: Amit K Dutta, Academic Fellow, Professor, Department of Gastroenterology, Christian Medical College, Ida Scudder Road, Vellore 632004, Tamil Nadu, India. akdutta1995@gmail.com
Received: April 8, 2025 Revised: April 18, 2025 Accepted: June 11, 2025 Published online: September 22, 2025 Processing time: 168 Days and 16.6 Hours
Abstract
BACKGROUND
Simultaneous assessment of gut microbiota in stool and tissue samples is crucial for a better understanding of their role in Crohn’s disease (CD), yet most reports have focused on fecal microbiota alone. Additionally, gut microbiota may serve as a clinically useful diagnostic biomarker of CD although data on this is limited.
AIM
To evaluate gut microbiota in tissue and stool samples in patients with active CD to understand the structure and function compared to healthy controls (HC). We also assessed their utility as a diagnostic biomarker of CD.
METHODS
Adult patients with active CD and HC were prospectively recruited for this study. The clinical and investigation details were recorded. Rectal mucosal biopsy and stool samples were obtained to assess the bacterial population. DNA was extracted, the V3-V4 region of the 16S rRNA gene was amplified, and library preparation was done and sequenced on the Illumina MiSeq platform. The bacterial diversity, composition, dysbiosis, predicted function, and predictors of disease state were estimated using the QIIME 2 pipeline and R packages.
RESULTS
We recruited 66 patients with CD (age 39.7 ± 11.1 years, 65.2% males) and 69 HC. Comparison of tissue with fecal microbiota in active CD showed significant differences in composition and predicted function. Both tissue and fecal microbiota from active CD showed reduced microbial diversity and compositional differences compared to HC, and disease state was a key determinant of bacterial population. Differences (CD vs HC) were noted in the abundance of several predicted synthetic and degradation pathways in both tissue and stool bacteria. Tissue microbiota was a superior predictor of active CD than stool (area under receiver operating characteristic curve 0.8 vs 0.62).
CONCLUSION
Gut microbial characteristics revealed significant structural and functional differences between CD and HC in both tissue and stool. Tissue bacteria performed well as a microbial biomarker for clinical diagnosis of CD.
Core Tip: Gut microbiota is emerging as a key player in the pathogenesis of Crohn’s disease (CD). The mucosal gut microbiota differs in structure and function compared to fecal microbiota, yet most studies have focused on fecal microbiota alone. We evaluated both mucosal and fecal microbiota in adults with active CD and compared this with the healthy controls. Our results show striking differences in bacterial structural and functional characteristics between mucosal and fecal samples in Crohn's disease. Additionally, the mucosal microbiota proved to be a good predictor of disease state and can serve as a novel potential biomarker for diagnosis of CD.
