Disease causing microorganisms are known as:
Pathogens
Pathogens are bacteria, virus, or other microorganisms that can cause disease are called pathogens.
Microbes can also be friendly, like the ones that are found in the intestines. These guys prohibit colonization by harmful ones.
Bacteriophages, also called phages or bacterial viruses, is any of a group of viruses that infect bacteria.
Amoeba is a eukaryote protozoan whose body most often consist of a single shapeless cell.