Unlike harmless microorganisms some microorganisms are harmful, that is they can make the host cell (plant, animal or human being) unwell.
Some microorganisms can cause illness in the host-cell; such microorganisms are called, pathogens.                
Notable disease caused by such pathogens are Mycobacterium tuberculosis, Streptococcus mutans. Streptococcus mutans is mostly found in teeth (oral cavity) of human beings that causes tooth decay.
Mycobacterium tuberculosis
Streptococcus mutans
Diseases that  spread from one infected (or) affected person to another healthy person are called Communicable diseases.
Some communicable diseases are the Common cold, Cholera, Typhoid, Dengue, etc.  Let's say if person is suffering from common cold with sneezing and coughing, The droplets of the infected person will have thousands of viruses that can be transmitted to another person when they both come in contact with each other.
Diseases like dengue are transmitted from one person to another person through carriers such as mosquitoes. The transmission is not through droplets of infected person but via blood. The female anopheles mosquitoes are most important carriers of dengue. The transmission of the disease can be through blood or food; that is if a mosquito bites an infected person, and it sits on the food that we are about to consume, that creates a chance of infection.

Some diseases caused by microorganisms in human beings
Diseases caused by microorganism in animals
Microorganisms can also cause damage to animals. One of the deadliest diseases in animals is anthrax caused by Bacillus anthracis. Foot and mouth diseases in animals caused by some viruses. Rabies is caused by viruses, and Q-fever is also a disease caused in animals by bacterias. Vaccination can be used to prevent animals from getting affected by rabies.
Diseases caused by microorganism in plants
Aster yellow and scab are diseased caused by bacteria. Plants are very sensitive to fungi. Some among them are Anthracnose, Canker, and Clubroot. Spotted wilt and mosaic are some of the viral diseases caused by microorganisms. Canker is mostly caused in citrus fruits such as lemon, oranges, and also known as Citrus Canker. An image of canker disease in lemon caused by a virus shown below.