The germ theory that has so modernised medicine and driven us, the western world living human to regard all bugs as bad has been undergoing a dramatic rethink over the last few years. Firstly the recognition that your body is teeming with bacteria, providing a warm residence to approximately 10 times as many bacterial cells as human cells. Our mutual inhabitants live on skin, in the respiratory tract and throughout the digestive tract. Your digestive tract alone is home to between 1,000 and 40,000 bacterial species depending on your choice of journal.
While some bacteria cause infections (see comprehensive wiki list here), most species are harmless or perform beneficial functions, such as aiding digestion. These beneficial bugs are called commensal bacteria. One of the most important functions of commensal bacteria is optimising the immune system. Studies by various researchers have found that mice raised in sterile, germ-free environments have poorly developed immune systems. Scientists are slowly pulling together the explanation for this.
The study in the Journal of Immunology published in May 2010 studied the spores from rod-shaped bacteria called Bacillus, found in the digestive tract. (A spore consists of the DNA of a bacterium, encased in a shell. Bacteria form spores during times of stress, and re-emerge when conditions improve.) Researchers found that when they exposed immune system cells called B lymphocytes to bacterial spores, the B cells began dividing and reproducing.
This group further found that molecules on the surfaces of the spores bound to molecules on the surfaces of B cells. This binding is what activated the B cells to divide and multiply. B cells are one of the key components of the immune system. They produce antibodies that fight harmful viruses and bacteria.
Two of the principle antibodies produce in the human gut is the immunoglobulin SIgA and SIgM and these are stimulated by the presence of the commensal and pathogenic bacteria as well as the non commensal yeast Saccharomyces Boulardii. These best understood immunoglobulin’s play a defensive role and a homeostatic role, as they facilitate the management of our commensal flora.
Other immunoglobulins IgE,IgG,IgD are also found in the mucosal tissues and whilst clinically these are sometimes controversial and difficult to measure as well as mediate’ it is clear that in relation to the mucosal immune system it can no longer be overlooked that these immunoglobulin’s have an important role in the spelling out of relevant mucosal defence strategies.
 Severson KM, Mallozzi M, Driks A, Knight KL. B cell development in GALT: role of bacterial superantigen-like molecules. J Immunol. 2010 Jun 15;184(12):6782-9. Epub 2010 May 7. View Abstract