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Updated: Sep 12, 2025
Non-invasive Assessment of the Efficacy of New Therapeutics for Intestinal Pathologies Using Serial Endoscopic Imaging of Live Mice
Published on: March 10, 2015
Combining mucosal microbiome and host multi-omics data shows prognostic potential in paediatric ulcerative colitis
Maria Kulecka1,2, Jill O'Sullivan1,2,3, Rachel Fitzgerald1,2
1APC Microbiome Ireland, University College Cork, Cork, Ireland.
Insights
Predicting ulcerative colitis relapse in children is possible using microbial and host data. Lower gut bacterial diversity and specific oral bacteria at diagnosis indicate higher relapse risk, enabling earlier treatment strategies.
Area of Science:
- Pediatric Gastroenterology
- Microbiome Research
- Immunology
Background:
- Current treatments for pediatric ulcerative colitis (UC) achieve remission in only 50% of cases.
- Early prediction of relapse could allow for timely immunosuppressant therapy.
Purpose of the Study:
- To identify predictive biomarkers for ulcerative colitis relapse in treatment-naïve children.
- To investigate the interplay between host factors and the gut microbiome in pediatric UC.
Main Methods:
- Collected intestinal biopsies from 56 treatment-naïve children.
- Performed quantitative microbial profiling, host epigenomics, transcriptomics, and genotyping.
- Conducted in vitro and in vivo experiments with selected bacteria.
Main Results:
- Lower baseline bacterial diversity and reduced butyrate producers were observed in relapsing children.
- Increased abundance of oral-associated bacteria, including *Veillonella parvula*, was linked to inflammation.
- Microbiota composition showed the strongest association with future relapse, followed by host epigenome and transcriptome.
- A machine learning model combining microbiome and epigenome data improved relapse prediction.
Conclusions:
- Host-microbe interactions hold significant prognostic potential for pediatric ulcerative colitis.
- Reduced colonic bacterial diversity in relapsing children may be exploited by pro-inflammatory oral bacteria.
Abstract:
Current first-line treatments of paediatric ulcerative colitis (UC) maintain a 6-month remission in only half of the patients. Relapse prediction at diagnosis could enable earlier introduction of immunosuppressants. We collected intestinal biopsies from 56 treatment-naïve children, combining mucosal quantitative microbial profiling with host epigenomics, transcriptomics, genotyping, and in vitro and in vivo experiments on selected bacteria. Baseline bacterial diversity is lower in relapsing children, who have fewer butyrate producers but more oral-associated bacteria, whereof Veillonella parvula induces inflammation in epithelial cell lines and IL10-/- mice. Microbiota has the strongest association with future relapse, followed by host epigenome and transcriptome. Interferon gamma signalling is also linked to relapse-associated bacteria. Relapse-prediction using separate omics data is outperformed by a robust machine learning approach combining microbiomes and epigenomes. In summary, host-microbe data have prognostic potential in paediatric UC. Our translational findings also suggest that pro-inflammatory oral-associated colonizers can exploit the reduced colonic bacterial diversity of relapsing children.
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