Colonic mucosal bacterial diversity of de novo extensive paediatric ulcerative colitis by next-generation sequencing
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Notice bibliographique
Résumé
Introduction Dysbiosis may contribute to inflammatory bowel disease (IBD) pathogenesis along with a reduced bacterial diversity. Limited bacterial diversity studies have been performed at the onset of disease in adults but rarely in children. High-throughput, parallel sequencing technology (next-generation sequencing) provides the means of assessing microbial diversity in samples from diverse ecosystems such as the colonic mucosa. Methods Paediatric patients undergoing colonoscopy were recruited to two groups: those with a new diagnosis of IBD at their first presentation and controls with a macroscopically normal colon and no evidence of IBD on biopsy. All subjects were free from systemic antibiotics, steroids and immunosuppression for 3 months. 5 extensive UC patients (E3) by Montreal criteria and 5 controls with macroscopically/microscopically normal colons were selected for assessment. The median age was 11.5 years in the UC group and 10.7 years in the controls. All patients were male. Colonic mucosal biopsies were taken from the rectum/sigmoid. DNA extraction was performed by a modified Qiagen QiAMP mini-kit method. The presence of bacteria was confirmed by universal eubacterial primers before next-generation PCR utilising V3 Forward/V6 Reverse primers. Bacterial diversity was assessed by 454 Titanium sequencing. Sequencing data was filtered, chimera and error checked and denoised before rarefaction to 13 000 reads per sample. Statistical comparisons were made by Mann–Whitney U tests using Sigma Plot 11. Results All biopsies were positive for bacterial DNA with universal eubacterial primers. The most commonly identified bacterial phyla (comprising 95.4% of sequence reads) were Bacteroidetes (45.3%), Firmicutes (40.5%) and Proteobacteria (9.7%). Bacteroidetes were significantly more common in the control colon than in UC (7641 median reads versus 4062, p=0.032) whereas Firmicutes were significantly more common in the UC colon than in controls (5471 median reads versus 3892, p=0.016). The difference between Proteobacteria was not significant (p=0.421). Bacterial diversity assessed by the Shannon index was similar in both groups (Medians of 6.1 in UC and 6.5 in controls, p=0.841). Conclusion Colonic mucosal bacteria differ between paediatric patients with extensive UC at diagnosis and controls. UC microbiota was typified by a reduction in Bacteroidetes and an increase in Clostridia . Surprisingly, a reduction in bacterial diversity is not present in extensive UC at diagnosis. This is contrary to findings from previous studies in established disease and warrants further investigation.
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Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,001 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découle