Humans are born into an environment laden with microorganisms, and colonization of the human body begins at the time of birth. Colonization simply implies the establishment of microorganisms on the body surface which, by extension, continues internally (oral cavity, gastrointestinal tract, ear canals, etc.). Throughout life, the skin and mucous membranes exposed to the outside world harbor a variety of indigenous bacteria, the normal flora.
A few hours after birth, the establishment of the normal flora on the surfaces of the body is well under way. Organisms acquired by an infant during passage through the birth canal are replaced by organisms derived from persons who attend the infant and from ingested foods. During the first day of life, many organisms find their niche for the life of the individual. Others take months or years to reach populations found in normal adults.
The number of different species of microorganisms living on the surfaces of the body is very large and even includes species that have not been fully characterized and classified. Some examples of the principal resident bacteria include Staphylococcus, Micrococcus and Propionibacterium found on the skin; Lactobacillus, Streptococcus, Neisseria, Corynebacterium and Bacteroides in the mouth; and Bacteroides, Clostridium, Lactobacillus, Streptococcus and many species of the Family Enterobacteriaceae in the intestinal tract. Usually the normal flora cause no disturbances in the health of their host. In fact, they often benefit the host by outcompeting pathogenic bacteria, yeasts and protozoa which are encountered occasionally
In the healthy individual it is not normal for microorganisms to grow in areas that are inside the body; the lungs, heart, brain, spleen and muscles are typically free of microbes. Penetration of these areas by the normal flora or pathogens will incur the wrath of the immune system and result in a diseased state. Your body has a vast array of defenses to keep microbes out of the internal regions and these are described in Animal Defenses Against Microbes in the microbiology textbook.
In the diagnosis of bacterial diseases of the human body, a general knowledge of the normal flora is essential. Exogenous pathogens must be distinguished from the indigenous species for the correct interpretation of bacteriological findings. Also, an increasing number of clinically-diagnosed bacterial diseases involves bacteria that are indigenous yet potentially pathogenic. Given an opportunity to infect an individual whose resistance is depressed, or, more specifically, to colonize an uncommon site (such as E. coli in the eye or urinary tract), certain of the normal flora may produce an endogenous bacterial disease. Examples of factors which lower the resistance of a host include radiation damage, prolonged use of antibiotics or steroids, and the debilitating effects of AIDS or other diseases. As the lives of more patients with major illnesses are prolonged by improved methods of treatment, and as more infections caused by virulent exogenous bacteria are controlled by effective antimicrobial drugs, endogenous bacterial diseases have become more common.
For more information on medically important bacteria, see Bacterial Pathogens in the microbiology textbook.