The hygiene hypothesis states that infections in early childhood expose a child to microorganisms that build up a child's immune system. Conversely, overprotecting the child to avoid infection and exposure alters the process, so that the individual is prone to having diseases where the immune process is out of control. Asthma is one example, but it's certainly not the only one. There are proposed mechanisms by which irritable bowel syndrome (IBS), psoriasis, and even diabetes, have possible origins as well.
The original hygiene hypothesis was proposed by Strachan in 1989. He observed that lower incidence of infection in early childhood could be an explanation for the rise in asthma and other allergic diseases in the 20th century.
It is also evident that the rise in asthma occurs in developed countries, while there's a low incidence in Africa and India, despite poor living conditions that one would think would result in respiratory ailments. The theory that polluted air in the industrialized countries explains incidence of asthma in those countries also falls short, since one of the countries with the highest mortality rate due to asthma is New Zealand, where there's no serious air pollution.
How our immune systems develop
To fully understand the hygiene hypothesis, one must understand how human immunity develops. There's a type of white blood cell (WBC) called lymphocytes. They are divided into two groups. One group known as B lymphocytes, produce antibodies. They are the early response, which is effective in containing the damage early in the infection process, but they are limited in their action.
Then there are the T lymphocytes that act using the whole cell, offering a more persistent and effective defense. This is a very intense response and requires a balance between two populations of cells - the "helper" cells, which induce the response, and the "suppressor" cells, which control the magnitude of the response. As an example, AIDS is caused by a virus that selects the helper T lymphocytes, making the individual susceptible to deadly infections.
The T helper cells are further divided into TH1 and TH2 cells. The TH2 cells drive the response and the TH1 cells fine tune and control the action of the TH2 cells. It is the exposure to bacteria in early life that stimulates the development of the TH1 cells. Conversely, poor or very limited exposure to bacteria will lead to less than adequate development of the TH1 cells. That will allow the TH2 cells to act unopposed. This leads to conditions that are characterized by over-activity of the immune system, such as occurs in asthma.
Why is bacteria important?
What is the importance of the bacteria that naturally colonize our bodies? You should know that there are three times as many bacterial cells than human cells in the body. Most of the bacteria (tens of thousands) are located in the gut. There are over 1,000 species of bacteria. They are important in generating enzymes that are essential in the biochemical reactions that occur in our body.
Recently, the use of probiotics or supplements that include certain bacteria to stimulate the gut population has become very popular. There's no clear evidence of its benefits in preventing disease. However, there is a clear relationship in the overuse of antibiotics and altering the bacterial population and development of certain diseases. Some doctors do recommend taking probiotics along with antibiotics or after a course of antibiotics, to restore the balance of microorganisms in the gut.
So bacteria are essential to the human processes. Altering their development either early in life or during adulthood will have significant consequences. Some of the consequences are predictable and treatable, while some will have an unknown effect. Science is still in the early stages of finding out those effects.