A German physician named Robert Koch (winner of the Nobel Prize in 1905 for this work with tuberculosis) was the first scientist to connect a specific bacteria to a certain disease. He established the following four criteria for identifying pathogenic bacteria. These criteria are still the guidelines for medical microbiology today.

1. The pathogen must be found in an animal with the disease and not in a healthy animal.
2. The pathogen must be isolated and grown in a laboratory.
3. When the isolated pathogen is injected into a healthy animal, the animal must develop the disease.
4. The pathogen must be isolated in the second animal, grown in the laboratory and identified as the same pathogen.

In an experiment in 1796, Edward Jenner injected cowpox into healthy individuals in an attempt to cause each person to develop immunity to smallpox. These experiments led to the modern vaccination process. A vaccine is a solution containing dead or modified pathogens which is injected into a healthy individual to create immunity to a particular disease. Smallpox was the first disease to be considered eradicated worldwide by vaccination (1977).

Allergic responses are initiated when antigens (such as pollen, mold spores or dust) attach to mast cells causing them to release histamines. Histamines increase blood flow and secretion of fluids, prompting a range of symptoms. 

Autoimmune disorders occur when the body cannot distinguish pathogens from its own cells and tissues. Multiple sclerosis, rheumatoid arthritis and systemic lupus are examples of autoimmune disorders.
 
Acquired Immune Deficiency Syndrome, or AIDS, is an example of what can happen when the immune system becomes compromised. When the AIDS virus (HIV) becomes active, it causes a person to become sick from diseases that a functioning immune system would prevent.

Bacteria were discovered in 1675 by Antony van Leeuwenhoek, but it wasn’t until 1876 that a German physician named Robert Koch first demonstrated that specific diseases are associated with particular microorganisms. Koch developed a set of criteria to show that anthrax, a disease of cattle, was caused by a specific bacterium, named Bacillus anthracis, and that tuberculosis was caused by a separate distinct bacterium. Koch presented his discovery of Mycobacteium tuberculosis in a lecture in March of 1882. He brought his entire laboratory setup to the lecture hall and demonstrated his procedures for his audience, inviting them to check his findings themselves. His methods were so innovative that his criteria still are useful today in identifying disease-causing agents. Difficulties in applying these criteria can arise, however, for agents that are difficult to grow in culture or where a suitable, susceptible experimental host cannot be found. This is an especially difficult situation, and raises ethical concerns, where humans are the only known host. Robert Koch was awarded the Nobel Prize in Physiology and Medicine in 1905 for his work in tuberculosis.

The majority of bacteria are not harmful and, in many cases, are beneficial to survival.  Prokaryotes are the decomposers of the Earth.  Many prokaryotes obtain energy by breaking down organic molecules and, in the process, make nutrients available for use by other organisms. Prokaryotes are the only organisms to metabolize inorganic nutrients such as sulfur, iron and nitrogen.  Nitrogen recycling, or nitrogen fixation, is unique to Prokaryotes and is the only biological mechanism that makes atmospheric nitrogen available for the production of organic compounds.  Mutualistic bacteria live inside our intestines aiding in digestion while other bacteria suppress the growth of yeasts and other microbes by altering pH levels in our body.
  
In the late 1800s, Louis Pasteur and other scientists linked bacteria to disease.  Robert Koch was the first to identify the organisms that cause tuberculosis and anthrax.  Since then, other pathogenic prokaryotes have been identified and linked to diseases, such Lyme's disease, tetanus, cholera, diarrhea, botulism and syphilis. In industry, bacteria have been used in bioremediation and as metabolic "factories" that produce acetone as well as pharmaceuticals like insulin and antibiotics.  Bacterial metabolic abilities are useful in separating sulfur compounds from copper and uranium in mining low grade ores.