The human microbiome and virome play important roles in health and disease by influencing immune regulation, metabolism, and host–microbe interactions. Increasing evidence suggests that microbial communities, including bacteria and viruses, are associated with the development and progression of multiple diseases such as neurodegenerative disorders, cancer, and liver diseases including hepatitis. These interactions may be particularly important in immunocompromised individuals, where microbial imbalance can influence susceptibility to infections and disease progression. This project aims to investigate microbial and viral community signatures across different disease contexts through the analysis of metagenomic sequencing datasets. Both newly generated sequencing data from research studies and previously generated datasets will be analyzed to characterize oral and gut microbiome and virome profiles. The study will explore microbial diversity, bacteriophage–bacterial interactions, and potential microbial markers associated with disease states. Computational analyses will be used to process large-scale sequencing datasets and to identify microbial and viral features that may contribute to disease mechanisms and immune dysregulation. By integrating microbiome and virome analyses across multiple disease contexts, this project aims to improve understanding of host–microbe interactions and their potential role in disease development.