Doctoral Thesis: Bioinformatics for Microbiome Analysis **Author:** Luis Fernando Delgado **Institution:** KTH Royal Institute of Technology, Stockholm, Sweden **Year:** 2024 Thesis Overview This doctoral thesis advances **bioinformatics methodologies** for the analysis of marine microbiomes, with a focus on microbial ecology, genomics, and population genetics, primarily in the Baltic Sea environment. It comprises four research papers addressing metagenomics, pangenomics, comparative genomics, and population genomics, supported by the development of novel computational pipelines and interactive tools. The work leverages cutting-edge next-generation sequencing (NGS) and bioinformatics to decode microbial diversity, functional potential, and pathogenicity factors, particularly for the bacterium Vibrio vulnificus. The research evaluates metagenomic assembly approaches for creating biome-specific gene catalogues, highlighting the effectiveness of the mix-assembly method in extracting information from metagenomic samples. A web-based tool, BAGS-Shiny, was developed to explore the Baltic Sea microbial gene set, facilitating reproducibility and broad applicability of the mix-assembly approach. The study also includes whole-genome sequencing of environmental Vibrio vulnificus strains, revealing insights into pathogenicity and adaptation mechanisms in response to changing environmental conditions.