Basic Study
Copyright ©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. Apr 14, 2023; 29(14): 2172-2187
Published online Apr 14, 2023. doi: 10.3748/wjg.v29.i14.2172
Changes in the gut mycobiome in pediatric patients in relation to the clinical activity of Crohn's disease
Agnieszka Krawczyk, Dominika Salamon, Kinga Kowalska-Duplaga, Barbara Zapała, Teofila Książek, Marta Drażniuk-Warchoł, Tomasz Gosiewski
Agnieszka Krawczyk, Dominika Salamon, Tomasz Gosiewski, Department of Microbiology, Division of Molecular Medical Microbiology, Jagiellonian University Medical College, Cracow 31-121, Poland
Kinga Kowalska-Duplaga, Department of Pediatrics, Gastroenterology and Nutrition, Jagiellonian University Medical College, Cracow 30-663, Poland
Barbara Zapała, Department of Clinical Biochemistry, Jagiellonian University Medical College, Cracow 31-066, Poland
Teofila Książek, Department of Medical Genetics, Jagiellonian University Medical College, Cracow 30-663, Poland
Marta Drażniuk-Warchoł, Department of Pediatrics, Gastroenterology and Nutrition, University Children's Hospital, Cracow 30-663, Poland
Author contributions: Krawczyk A performed the molecular investigations, interpreted the data, prepared the tables and figures, and wrote the manuscript; Kowalska-Duplaga K recruited patients, and revised the paper; Zapała B analyzed data, and revised the paper; Książek T performed the investigations; Drażniuk-Warchoł M recruited patients; Salamon D, and Gosiewski T coordinated the study, interpreted data, and revised the article; all authors approved the final version of the article.
Supported by National Science Centre (Poland), No. 2019/33/N/NZ5/00698.
Institutional review board statement: The study was reviewed and approved by the Jagiellonian University Bioethics Committee, No. 1072.6120.21.2020.
Informed consent statement: All participants received explanations about the study objectives and expected results, having been enrolled in the study only after signing the informed consent form.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
Data sharing statement: Fastq files are available from The Jagiellonian University Repository-online access:
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (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: Tomasz Gosiewski, MSc, PhD, Full Professor, Department of Microbiology, Division of Molecular Medical Microbiology, Jagiellonian University Medical College, Faculty of Medicine, Czysta 18 Str., Cracow 31-121, Poland.
Received: December 21, 2022
Peer-review started: December 21, 2022
First decision: January 3, 2023
Revised: January 13, 2023
Accepted: March 9, 2023
Article in press: March 9, 2023
Published online: April 14, 2023
Research background

The recurrent and chronic course of Crohn’s disease (CD), its systemic after effects, and intestinal complications constitute a serious clinical problem, and since the pathogenesis of the disease is unknown, causal treatment is currently not used. As CD incidence age keeps falling and there is a growing number of cases, we are led to undertake intensive studies to determine the possible causes of this disease. Recently, due to the growing interest in the topic of intestinal microbiome, a hypothesis has emerged that the initiation of CD is associated with dysbiosis within the gut microbiota. And while the importance of bacteria in the pathogenesis has been, up to now, a common subject of research, the involvement of fungi has usually been overlooked. The few available studies including mycobiome analysis concern adults and not children, previously treated patients, or those with long-term disease. These shortcomings distort the results due to the impact of confounding variables (such as treatment, age, or the long-term disease process) on changes in the fungal composition.

Research motivation

Undoubtedly, the composition of the microbiome has a significant influence on maintaining internal balance and health and microbial changes constitute an important factor inducing pathological processes. Due to the fact that fungi are an important component of the gut microbiota, it is possible that alterations in the composition of the gut mycobiome may have an impact on the induction of CD.

Research objectives

Taking into account the likely relationship between the mycobiota and the host, the aim of this study was to perform a detailed taxonomic analysis of the fungal composition in pediatric patients with CD. In our study, we recruited children and adolescents with newly and previously diagnosed CD and compared their mycobiome in the exacerbation and remission periods. Additionally, we recruited healthy children into a control group. Such a study allowed for a more reliable determination of the relationship between fungi in the digestive tract and the course of CD.

Research methods

DNA was isolated from stool samples from patients: With active, newly diagnosed CD (n = 50); active but previously diagnosed and treated CD (n = 16); non-active CD who were in clinical remission (n = 39) and healthy volunteers (n = 40). The next step was to prepare genomic libraries for next generation sequencing (NGS). NGS was performed using a MiSeq sequencer (Illumina). The composition of the gut mycobiota was analyzed using UNITE Fungal ITS Database v7.2, and then correlated with clinical and blood parameters.

Research results

Our study confirms alterations in fungal composition in pediatric CD patients and shows that some species of fungi may be a kind of microbiological marker related to the activity of the disease. In CD patients, we have documented an increased load of fungi with potential pro-inflammatory effects (e.g. Candida spp., Malassezia spp.), while fungi with potential anti-inflammatory effects (such as Saccharomyces) were found in a lower percentage. Interestingly, the greatest alterations in mycobiome composition (compared to the control group) were observed among newly diagnosed patients, before implementing any therapeutic approaches. This is strong evidence that fungi may play an important role in the development of CD. This thesis is supported by the fact that a positive correlation of some species with calprotectin or pediatric CD activity index was documented. Furthermore, owing to linear discriminant analysis, we have shown that some fungal species could be biomarkers characterizing and distinguishing a given group of patients (depending on the disease activity) which in the future may be helpful in predicting an exacerbation of the disease or even predicting the diagnosis of CD.

Research conclusions

Changes in the composition of the intestinal mycobiome occur already at the beginning of the disease (in newly diagnosed and untreated patients). Furthermore, the composition of fungi changes depending on the activity of CD.

Research perspectives

Further research should focus on selecting fungal species that could be biomarkers to help predict disease exacerbation. Furthermore, next research should assess whether the fungal mycobiota could be a therapeutic target.