Pathogenic organisms Pathogenic Microorganisms. Microorganisms and Pathogenicity Microorganisms are tiny living organisms that can be found in diverse environments. Some of these organisms are pathogenic, meaning they can cause diseases in humans, animals, and plants. Pathogenic microorganisms include bacteria, viruses, fungi, protozoa, and helminths. Among these, bacteria are classified into various categories based on their shape, staining properties, and metabolic characteristics. Bacterial Classification Based on Gram Staining The Gram stain