Numerous commensal microorganisms inhabit healthy human bodies.

The main purpose of the immune system is to protect the human body from infectious disease. Almost all infectious diseases suffered by humans are caused by microorganisms smaller than a single human cell. For both benign and dangerous microorganisms alike, the human body constitutes a vast resource-rich environment in which to live, feed, and reproduce. More than 500 microbial species live in the healthy adult human gut and contribute about two pounds to the body's weight; they are called commensal species, meaning they 'eat at the same table.' The community of microbial species that inhabits a particular niche in the human body-skin, mouth, gut, or vаginа- is called the flora, for example the gut flora. Many of these species have not yet been studied properly because they cannot be propagated in the laboratory, growing only under the special conditions furnished by their human hosts.

Animals have evolved along with their commensal species and in so doing have become both tolerant of them and dependent upon them. Commensal organisms enhance human nutrition by processing digested food and making several vitamins. They also protect against disease, because their presence helps to prevent colonization by dangerous, disease- causing microorganisms. In addition to simple competition for space, Escherichia coli, a maj or bacterial component of the normal mammalian gut flora, secretes antibacterial proteins called colicins that incapacitate other bacteria and prevent them from colonizing the gut. When a patient with a bacterial infection takes a course of antibiotic drugs, much of the normal gut flora is killed along with the disease - causing bacteria. After such treatment the body is recolonized by a new population of microorganisms; in this situation, opportunistic diseasecausing bacteria, such as Clostridium difficile, can sometimes establish themselves, causing further disease and sometimes death (Figure 1.A) . C. difficile produces a toxin that can cause diarrhea and, in some cases, an even more serious gastrointestinal condition called pseudomembranous colitis.

When antibiotics are taken orally to counter a bacterial infection, beneficial populations of commensal bacteria in the colon are also decimated. This provides an opportunity for pathogenic strains of bacteria to populate the colon and cause further disease. Clostridium difficile is an example of such a bacterium; it produces a toxin that can cause severe diarrhea in patients treated with antibiotics. In hospitals, acquired Clostridium difficile infections are an increasing cause of death for elderly patients.

Figure 1.A. Antibiotic treatments disrupt the natural ecology of the colon.