The microscopic world of viruses, bacteria, protozoa and other tiny living beings is extremely fascinating and diverse, and microorganisms are omnipresent in our daily lives. Our skin, mouth and gut are colonized by trillions of harmless bacteria that protect us from the invasion by pathogens and help us digest our food. We are transforming food with the help of bacteria and yeasts, such as cheese, yoghourt, sauerkraut, bread, wine and beer. No biogeochemical cycle in the world is complete without the unique metabolic capacities of microorganisms. Our domestic wastewater is treated in sewage treatment plants, where many different microorganisms get rid of people’s poo and urine, medication and food residues. Nevertheless, besides the vast majority of essential and totally harmless microorganisms, some viruses, bacteria, parasites and fungi are pathogenic and can cause severe disease in animals and humans. To date, more than 1,400 different infectious microbes have been identified. Our public health system historically has been built upon the issues created by these tiny troublemakers, sometimes causing important outbreaks and pandemics worldwide.