The distribution of the microbiota within the digestive tract depends a great deal on the ability of bacteria to adhere to the walls of the intestinal epithelium. Bacteria showing better adhesion properties are characterized by having a membrane composed almost entirely of saturated fats with a significant presence of myristic acid. These fatty acids bind to enzymatic proteins (kinases) embedded in the plasma membranes of enterocytes (intestinal epithelial cells) and enable the cell and bacterium to bond like a firm handshake.


The fatty acids composition of each microorganism facilitates, or not, the ability of lactic acid bacteria—including those in food supplements—to form stable colonies in the gut.
The distribution of the microbiota in the gut somewhat follows the different adhesion abilities.


The stomach environment is not very suitable for life but, contrary to what one might think, it is not sterile. A large number of bacteria such as Streptococcus, Veillonella, Helicobacter pylori or various Lactobacilli such as Lactobacillus acidophilus, live and proliferate in the submucosal layer. These bacteria often compete for the same few resources and keep the gastric environment healthy. The bacterial concentration per gram of tissue in the stomach is about 102.


Duodenum, jejunum and ileum are richer—but not so crowded—environments. This tract has very important organizational functions since hormones such as cholecystokinin, secretin and motilin are produced here. Bacillus, streptococci, Bacteroides, Clostridium and Bifidobacteria live and proliferate in the small intestine. Bifidobacteria preside over the cellular junctions within the Lieberkühn crypts and help regulate the permeability of the gut. In this tract the concentration of bacteria per gram ranges from 104 to 107.


The primary daily activity of the microbiota in the colon is to oversee the proliferation of unwanted bacteria and produce vitamins, enzymes and short-chain fatty acids (see maintenance of eubiosis). The oldest, most fragile and well-preserved microbiota core and a large number of SCFA-producing bacteria such as Roseburia, Faecalibacterium, Fusobacteria and Eubacterium live between the cecum and the colon. The concentration of bacteria per gram in this area reaches 1012.


In addition to the longitudinal distribution along the major axis of the gastrointestinal tract, the microorganisms of the microbiota are also axially arranged from the lumen to the surface of the inner lining mucosa. This distribution often depends on the oxygen gradient: for example, Bifidobacteria live in areas, such as crypts, with the poorest oxygen levels, while areas like epithelial surfaces, which are richer in oxygen, are better adapted for facultatively anaerobic bacteria like Lactobacilli.


Each bacteria species in the microbiota occupies its own "ecological niche". Likewise, each food supplement based on lactic acid bacteria has different microbiological characteristics and interacts in a precise manner within a specific intestinal ecological niche!