A wide variety of microorganisms interact with humans, exploiting a wealth of micro-environments. Certain parts of the body are sterile. These include the solid organs, blood, cerebrospinal fluid, and urine. The lower respiratory tract in health is also sterile. This sterility in an open system is due to the action of the "mucociliary escalator" that sweeps foreign matter back out of the lungs. Exposed sites are colonised by large numbers of microorganisms that are highly adapted to their particular environment. These organisms constitute the body's normal flora.

In diagnostic microbiology, it is important to distinguish between a patient's commensal flora, and the causative agent of the infection from which they are suffering. This is not always an easy process, since in some cases microbes are normal flora at certain anatomical locations, but are considered pathogens when isolated from other sites.

Most of the microbes discussed are bacteria, although some fungi and certain protozoa also contribute the human commensal flora. Viruses are a special case. There is still debate concerning the nature of viruses, and certainly they are structures that are incapable of autonomous existence. In many cases virus infection is entirely to the detriment of the host. However, certain viruses have the ability to form latent infections. A good example of a virus that causes a latent infection is the herpesvirus herpes simplex 1 or HSV 1. This virus infects the vast majority of humans some time during early childhood, and often the primary infection is inapparent. It infects the mucous membranes around the mouth, and the virus spreads to the trigeminal ganglion. There it enters a latent phase. The virus DNA persists, but there is little or no production of novel virus particles. When the host is subjected to stresses of various kinds, the latent virus can undergo a reactivation. New virus particles are produced, and these spread back to the mucous membranes around the mouth, where they erupt to cause the characteristic "cold sores", suffered by a number of people. Certain individuals are more prone to develop cold sores than others are, but the majority of people world-wide carry HSV 1 as a latent infection. Because it is so widespread, and because, at least for the majority of the time it causes so few problems, it has been argued that HSV 1 and other latent viruses may be considered as commensal with humans.

The vaginal flora changes dramatically through life. When a baby girl is born, she still carries her mother's hormones for a short while, and the vaginal flora is dominated by lactobacilli, sometimes called "Döderlein" bacilli. As the maternal hormones decline, the flora changes to resemble the bowel flora. However, with the onset of puberty reproductive hormones are produced, and the lactobacilli return. At the menopause the flora reverts to resemble the bowel flora once more.

When members of the commensal flora from one anatomical site gain access to a different location then infection may result. Sometimes these are relatively trivial, but others may be life-threatening. Such infections are known as endogenous. From where do you think the bacteria that cause the following infections originate, and what is the most likely cause in each case?

Gram-positive bacteria contain large quantities of peptidoglycan. This is a polymer that confers considerable mechanical strength on the wall, enabling bacteria to withstand considerable pressures, including osmotic pressures. In contrast, Gram-negative bacteria contain very little peptidoglycan in their cell walls.