Protective roles of the upper digestive tract and small intestine

The upper digestive tract has several innate defences to protect you from your own secretions and from microbial invaders. These defences include mucus and gastric acid, enterosalivary nitrate circulation, peristalsis and lymphoid tissue in the form of Peyer’s patches. Mucus, a bicarbonate-rich slimy substance secreted by superficial epithelial cells throughout your stomach, protects you from foreign microbes, and protects you from your gastric acid. In general, bacteria and other microbes that you ingest are destroyed by their exposure to gastric (stomach) acid (Shaffer, 1997; Holzapfel et al., 1998; Dunne et al., 2001; Guarner & Malagelada, 2003). For this reason, the stomach is viewed as the main barrier against entry of foreign microbes into the gastrointestinal tract. However, it is important to note that, even with its acidic environment, the stomach is not sterile.

Not chewing your food properly leads to reduced peristalsis and reduced production of gastric acid and saliva (O’May et al., 2005a, b). Inorganic nitrate ingested as part of the diet is absorbed in the stomach and ~25 % is concentrated in the salivary glands and re-secreted into the mouth (Deri et al., 2005). Around 30 % (~0.3 mM) of this nitrate is reduced to nitrite by the oral microbiota on the tongue (O’May et al., 2005a, b; Deri et al., 2005). Acidification of the nitrite in the stomach generates nitric oxide: at the gastric level, this molecule has antibacterial properties, and increases gastric motility, mucus production and mucosal blood flow (Deri et al., 2005).

Breakdown of the aforementioned defence mechanisms leads to bacterial overgrowth in the upper gastrointestinal tract (stomach and duodenum) (O’May et al., 2005a, b), with the degree of overgrowth dependent upon the elevation of the gastric pH (Kerckhoffs et al., 2006).

In addition to the numerous defence mechanisms associated with the stomach, protection of the rest of the digestive tract from foreign microbes comes in the form of hepatic and pancreatic secretions and secretions from the small intestine. Bile acids are synthesized (500–700 ml per day) by the liver from cholesterol and secreted from the liver or gallbladder into the duodenum in the conjugated form (Dunne et al., 2001). These bile acids are chemically modified (i.e. deconjugated, dehydroxylated, dehydrogenated or deglucuronidated) by gut bacteria. Both conjugated and deconjugated forms of bile acids have been shown to have antibacterial properties, with the deconjugated forms being more inhibitory and Gram-positive bacteria more sensitive than Gram-negative bacteria (Dunne et al., 2001). The difference in sensitivity between Gram-positive and Gram-negative bacteria is largely due to differences in the composition of their cell walls. An intact ileocaecal valve is also an important barrier to backflow of colonic bacteria into the ileum (Kerckhoffs et al., 2006).

​References
Deri, L., Pietraforte, D., Scorza, G., Napolitano, A., Fogliano, V. & Minetti, M. (2005). Apples increase nitric oxide production by human saliva at the acidic pH of the stomach: a new biological function for polyphenols with a catechol group? Free Rad Biol Med 39, 668–681.
Dunne, C., O’Mahony, L., Murphy, L. & 11 other authors (2001). In vitro selection criteria for probiotic bacteria of human origin: correlation with in vivo findings. Am J Clin Nutr 73 (suppl.), 386S–392S.
Guarner, F. & Malagelada, J.-R. (2003). Gut flora in health and disease. Lancet 361, 512–519.
Holzapfel, W. H., Haberer, P., Snel, J., Schillinger, U. & Huis in’t Veld, J. H. J. (1998). Overview of gut flora and probiotics. Int J Food Microbiol 41, 85–101.
Kerckhoffs, A. P. M., Samson, M., van Berge Henegouwen, G. P., Akkermans, L. M. A., Nieuwenhuijs, V. B. & Visser, M. R. (2006). Sampling microbiota in the human gastrointestinal tract. In Gastrointestinal Microbiology, pp. 25–50. Edited by A. Ouwehand & E. E. Vaughan. New York: Taylor & Francis Ltd.
O’May, G. A., Reynolds, N., Smith, A. R., Kennedy, A. & Macfarlane, G. T. (2005a). Effect of pH and antibiotics on microbial overgrowth in the stomachs and duodena of patients undergoing percutaneous endoscopic gastromy feeding. Appl Environ Microbiol 71, 3059–3065.
O’May, G. A., Reynolds, N. & Macfarlane, G. T. (2005b). Effect of pH on an in vitro model of gastric microbiota in enteral nutrition patients. Appl Environ Microbiol 71, 4777–4783.
Shaffer, E. A. (1997). Digestive system, physiology and biochemistry. In Encyclopedia of Human Biology, 2nd edn, vol. 3, pp. 343–354. Edited by R. Dulbecco. San Diego, CA: Academic Press.