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 that cause harm to living organisms or host-cell are called pathogens.                
Some important disease-causing pathogens are Mycobacterium tuberculosis, Streptococcus mutans. Streptococcus mutans is mostly found in teeth (oral cavity) of human beings and causes tooth decay.
Mycobacterium tuberculosis
Streptococcus mutans
Communicable diseases
Diseases that can be 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, while sneezing the droplets of the infected person will have thousands of viruses which can be transmitted into another person's body if they both are close to 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 through the blood. The most important carriers of dengue are female anopheles mosquitoes. The transmission of the disease can be through blood or even through food, that is if a mosquito bites an infected person and it sits on the food that we are about to consume, we may be infected with the same.
Some diseases caused by microorganisms in human beings
Some diseases in animals caused by microorganisms
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 are 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.
Some diseases in plants caused by microorganisms
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 known as citrus canker. Below is the image of canker disease in lemon caused by a virus.