The 25-35 foot long GI tract of an adult human is estimated to harbour about 100 trillion viable bacteria. This is approximately 10 times the total number of cells in the human body. These live bacteria account for around 2 lbs of a body’s weight and are known as intestinal or gut flora. Viruses, fungi and protozoa can also be present, but these normally form only a minor component of the total resident population of micro-organisms in healthy individuals.
The density of micro-organisms in the gut flora increases dramatically from 10-1,000 CFU/ml (Colony Forming Units basically mean live bacteria) in the stomach to 10-100 billion CFU/gm in the large intestine and these belong to as many as 400 different species. Anaerobic bacteria outnumber aerobic bacteria by a factor of 1000:1. Anaerobic flora is dominated by Bacteroides spp., bifidobacteria, propionibacteria and clostridia. Among aerobic and anaerobic bacteria, enterobacteria, (mainly E.coli), and enterococci predominate.
Bacteria have been estimated to constitute 35-50% of the volume of the contents in the human colon. They profoundly influence nutritional, physiologic and protective processes. Both direct and indirect defensive functions are provided by the normal microflora. Specifically, gut bacteria directly prevent colonization by pathogenic organisms by competing for essential nutrients or for epithelial attachment sites. By producing antimicrobial compounds, volatile fatty acids, and chemically modified bile acids, indigenous gut bacteria also create a local environment that is generally unfavourable for the growth of enteric pathogens. This phenomenon is called Colonization Resistance, which can be defined as the ability of micro-organisms belonging to the normal gut microflora to impede the implantation of pathogens. This function of the microflora is also known as the barrier effect. While probiotic bacteria improve colonization resistance, consensus thinking is that the importance of lactic acid bacteria as probiotic agents lies more in the indirect mechanisms such as immunomodulation.
The normal or indigenous microflora of man consists of a resident (autochtonous) part, which largely stays with the host organism, and a transient part, which may dynamically change in composition. This is not unique for man as it also applies to animals. The turnover of the transient part of the microflora of the digestive tract depends both on the composition of the resident flora or Colonization Resistance, and on the degree of contamination (both qualitatively and quantitatively) of ingested food and beverages. Regarding the latter, hygienic conditions of the environment are important.
The defence systems in the gut can be divided into three parts: the gut flora, the gut mucosa and epithelium and the related immune system.
The intestine, composed of villi and crypts, is coated with mucus that protects the intestinal cells. At the bottom of the crypts lie specialised cells known as Paneth cells that are able to release antimicrobial molecules into the gut lumen. The intestinal flora, present mainly in the colon, forms a natural barrier to pathogens. The intestinal immune system comprises cells disseminated beneath the epithelium and also between epithelial cells (intraepithelial lymphocytes). Lymphocytes are also found within more organised structures, lymphoid follicles, with a central region of B lymphocytes and a lateral region of T lymphocytes. Above these structures, we find M cells, which are specialised in transporting particles to the follicle. These areas of the intestine are known as Peyer’s patches. When a lymphocyte is activated by a dendritic cell presenting an antigen, it leaves the mucosa in lymph and enters the bloodstream via the thoracic canal. This activated lymphocyte then colonises either the same mucosa or other mucosal effector sites.