In this project, we will carry out analyses of bacterial genome sequences for purposes spanning from the identification of mobile genetic elements conferring antibiotic resistance to eco-physiological studies. Our team has a track record of publications on phylogenomics and comparative genomics. We have obtained competitive funding to delve into the dissemination of antibiotic resistance genes in waterborne bacterial populations of clinical significance for both humans and animals. Exemplary key bacterial genera for us are Shewanella, Vibrio, Aeromonas, and the family Enterobacteriaceae. We also have funding for the study of physiological adaptations of bacterial populations to environmental or host-associated niches. At present, we already have several hundreds of bacterial genome sequences obtained mostly in-house at Karolinska Institutet and we plan to increase substantially this number in the frame of our ongoing investigations, which include the obtaining of complete bacterial genomes and epigenomes for comparative, functional, and evolutionary studies. We are also undertaking efforts on environmental metagenome sequencing for the identification of circulating antimicrobial resistance genes and the analysis of microbial metabolic functions from a variety of samples.