Complex interactions between different environments, between animals and humans, microbes or genes and their products affect infectious disease dynamics and the epidemiology of pathogens. The projects in the NCOH PhD tract topic “Complex systems & Metagenomics” tackle different aspects of these interactions, such as transmission of microbial strains or mobile genetic elements, susceptibility to infection and selection for resistant microorganisms. Current methods describing the epidemiology of pathogens generally focus on analysis of single isolates. In this topic we will investigate the use of metagenomics analysis of the microbiome including fungi and viruses at the animal-human-environmental interface. We aim to develop novel methods to describe the complex dynamics of dissemination of (antibiotic resistance) genes and pathogens. We will examine effects on the development of (infectious) disease or syndromes, host processes, and on the environment as emissions.