Data-Driven Analysis of Microbial Community Dynamics in Inflammatory Bowel Diseases

This work is focused on a detailed analysis of gut microbiome changes in Inflammatory Bowel Disease (IBD) patients, under a specific treatment regime. The study includes practical work with QIIME2, a bioinformatics software, for taxonomic classification based on 16S sequencing data. Additionally, the student will engage in the construction and interpretation of gene content networks for functional annotation of the microbiome. The thesis utilizes data collected from 140 IBD patients (60 with Crohn's Disease and 80 with Ulcerative Colitis) from the DISCOG group at Padova Hospital. These patients were treated with oral microencapsulated sodium butyrate (BML) for three months, alongside their usual therapies. The impact of this treatment is assessed through analyses of stool samples, which were collected at the start (T0=0 day) and end (T1=90 days) of the treatment period. These samples underwent 16S sequencing and faecal calprotectin analysis, providing insights into the microbial composition and inflammation levels. In addition to the microbiome analysis, the thesis involves evaluating the clinical disease activity of the patients using standard clinical methods at both T0 and T1. The main aim of this study is to determine how BML treatment affects the microbiome composition in IBD patients and to understand its role in modifying the disease activity.