The occurrence of microorganisms such as bacteria in our gastrointestinal tract is sparse in our mouth and stomach, and almost non-existent in our small intestine. However bacteria is luxuriant in the lower bowel (colon) where they live in huge populations and most assist the health of the body (the gastrointestinal tract is a part of the external environment in the form of a tube coursing through our body proper).
Inside the colon live hundreds of species of commensal bacteria which create for our bodies K2 vitamin and some of the B-vitamins (biotin, vitamin B12, folic acid, and thiamine), that we cannot get from cooked foods—and indeed we cook most of our foods. These friendly bacteria also recycle essential bile chemicals that our liver produces (bilirubin, bile acids, cholesterol, estrogens, as well as liver "drugs" such as morphine) and the metabolites of vitamin-D. The bacteria also play a small role in fiber reconstitution for suitable stool formation.
Our immune system "farms" and "feeds" these bacteria according to the seasons and the type of micronutrition our body needs to stay healthy from week to week. Alongside and among these desired colon bacteria hide pathogenic microorganisms that continually test our immune system's capabilities to remove them. Bacteria such as Vibrio cholerae, E. coli, Shigella and Campylobacter, Bacteroides, Anaerobic Streptococci, Clostridia, along with Rotavirus, Calicivirus, as well some forms of protozoa and thread worms, as well as other undesirables.
Gastric acid in the stomach kills most organisms that come along with our food. People with reduced gastric acid usually have some bacterial colonisation in the small intestine and are then more susceptible to bacterial diarrhoeal disease. Liver bile has antibacterial properties and helps control unwanted bacteria in the small intestine. The good bacteria of the colon also produce their own antibacterial substances (e.g., bacteriocins and fatty acids), to stop pathogenic bacteria from dominating their community.
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