Published online Apr 14, 2023. doi: 10.3748/wjg.v29.i14.2172
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
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.
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.
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.
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.
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.
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.
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.