The gut microbiome and resistome in clinical transplant studies

This dissertation investigates the interactions between the gut microbiome and hematopoietic stem cell transplant (HCT), with the goal of helping us understand microbial diversity and their functional implications in HCT outcomes. The dissertation is composed with three main projects: 1) analysis of gut microbiota diversity in patients with Graft-versus-Host disease (GVHD), 2) examination of the effect of care given and infusion site on gut microbiome composition and antimicrobial resistance gene diversity, and 3) a focused evaluation of differential abundance analysis (DAA) methods for microbiome data, including DESeq2, edgeR, t-test, and Wilcoxon test.
To achieve these objectives, we have employed high-throughput sequencing techniques, different bioinformatics tools and statistical analysis. The main findings of these projects include observable differences in certain microbial species and calprotectin levels between GVHD statues; site specific variations in microbiome composition for HCT patients; and insights into the performance and suitability of different statistical methods for microbiome data DA analysis.
Our results highlight the importance of considering microbial diversity in HCT and provide insights in improving patient outcomes through microbiome analysis. Additionally, our findings emphasize the importance of carefully selecting the statistical methods in microbiome studies to ensure accurate interpretation of differential abundance analysis results. This dissertation aims to contribute to add knowledge on microbiome research and show potential directions for future studies.