Dottorato in TECNOLOGIE BIOMEDICHE INNOVATIVE IN MEDICINA CLINICA

Titolo della tesi: FECAL AND MUCOSAL MICROBIOTA PROFILING IN CHILDREN WITH INFLAMMATORY BOWEL DISEASE AND IRRITABLE BOWEL SYNDROME

Background and aims: Recent research evidence support the role of gut mucosal microbiota in the mechanisms underlying both organic and functional diseases. However, few studies have been conducted in children, and most of them focused on fecal microbiota only. Mucosa microbiota seems to belong to a distinct niche and, due to its closeness to the enterocytes, could play a decisive role in interactions with the immune system. Therefore, this study aimed at evaluating and describing mucosal and fecal microbiota in children with inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) compared to healthy controls (CTRLs). Secondary aims were to perform an intra-individual evaluation between inflamed (IBD-I) and not inflamed (IBD-NI) colon mucosa microbiota in IBD patients; to compare fecal microbiota and mucosa microbiota within each study group; to conceive possible microbial “biomarkers” of disease and health in children with IBD and IBS. Patients and Methods: Fecal and colonic samples from children with IBD, IBS, and CTRLs were analyzed. The relative abundance of bacteria at phylum and genus/species levels and bacterial diversity were evaluated through 16S rRNA sequence-based of fecal and mucosal microbiota analysis. Results: A total of 123 subjects were recruited in the study: 59 (48%) IBD patients (26 with Crohn’s disease and 33 with ulcerative colitis), 25 (20.3%) IBS patients, and 39 (31.7%) CTRLs. Increasing values of microbial diversity were recorded going from IBD to IBS to CTRLs in fecal samples. β-diversity analysis showed a clear separation between groups both in feces and in mucosa, although the difference was not significant between IBS and CTRLs, and between IBD-I and IBD-NI in mucosa samples. At phylum level the fecal microbiota analysis of IBD patients showed an increment of Proteobacteria, Actinobacteria and Fusobacteria and a decrease of species with anti-inflammatory properties (i.e. Bacteroidetes) compared to CTRLs. Analogously, the latter where reduced in IBS patients when compared to CTRLs; however, when compared to IBD, IBS patients showed higher abundance of Bacteroidetes and Verrucomicrobia. At genus/species level a predominant presence of Haemophilus parainfluenzae was observed in IBD, especially among UC patients; Sutterella was more abundant in IBS; Oscillospira, Ruminococcus, Clostridium and Bifidobacterium were predominant among CTRLs. Mucosal microbial composition was characterized at phylum level by an increment of Actinobacteria in IBD if compared to CTRL. Bacteroidetes were significantly decreased in IBD patients compared to IBS. At genus/species level, Faecalibacterium prausnitzii was predominant in IBD mucosal samples, while Dorea, R. gnavus and Bacteroides fragilis were enriched in CTRLs. IBD-I group showed increased abundance of Fusobacterium compared to IBD-NI. Prevotella copri and Haemophilus parainfluenzae resulted increased in IBS. β-diversity analyses showed a significant separation between fecal and mucosa samples in all study groups. Conclusions: Significant alterations in gut microbiota profile were recorded in our IBD and IBS pediatric patients, in whom a decrease of species with anti-inflammatory properties was detected, although primarily among IBD patients. Surely, these are preliminary data, that need to be further confirmed in larger cohort. Plausibly, in the next future the analysis of gut microbiota could help in the diagnosis and management of children with organic and functional diseases.