Emiliano Pereira

• Microorganisms encompass a vast metabolic and genetic diversity and are key drivers of ecosystem functioning. Metagenomics, by allowing access to the genomic material obtained directly from the environment, represents a major field of research in microbiology. The recent advent of high-throughput sequencing technologies has pushed the scale and scope of metagenomic studies. Today more than ever, metagenomics is critical to advance our knowledge of microorganisms. The research work presented in this thesis develops two (interconnected) lines of research in the field of metagenomics. The first of these is the study of natural product Biosynthetic Gene Clusters (BGCs). Microorganisms encode a large diversity of BGCs responsible for the production of several compounds with valuable industrial applications. BGCs are also important from an ecological perspective, as these participate in interactions between organisms and with the environment. To improve the exploitation of metagenomic data in BGC exploration analyses, we developed the Biosynthetic Gene Cluster Metagenomic Exploration toolbox (BiG-MEx). BiG-MEx is able to rapidly estimate the BGC domain and chemical class composition of a metagenomic sample, and perform a series of domain diversity analyses. The second research line developed in this thesis is the application of functional trait-based approaches in metagenomics. Functional traits provide valuable information to study different aspects of microorganisms’ ecology. We developed a series of tools to quantify different metagenomic functional traits, including the average genome size, 16S rRNA gene average copy number, functional diversity, and percentage of transcription factors, among others. In conclusion, this thesis contributes to the advancement of BGC mining analyses and the application of functional trait-based approaches in metagenomics.