The Microbiota of Human GI Tract

Bacteria are normal cohabitants with humans, being associated with several tissues such as skin, vaginal, respiratory, and gastrointestinal (GI) tracts. The intestinal tract is a dynamic ecosystem that is influenced by host, intrinsic, and environmental factors. The microbial community inhabiting the GI tract is characterized by its high population density, biodiversity, and complexity of interactions. Bacteria are predominant, but a variety of protozoans, yeasts, and bacteriophages may be present as well. They are not distributed randomly thoughout the GI tract but are found at population levels and species distribution characteristic of specific regions of the tract.

Bacteria do not generally colonize the stomach in high numbers because of low pH and rapid transit. The stomach of healthy adults contains around 103 bacteria per gram, the main genera being Lactobacillus, Enterococcus, Helycobacter, and Bacillus (ILSI Europe, 2013).

Table Examples of Microorganisms with Found Beneficial Effects.


Beneficial effect/s

Lactobacillus rhamnosus GG (ATCC-53103)

  • • Immune modulation
  • • Prevention of urogenital infections
  • • Prevention of diarrhea of C.difficile
  • • Prevention of diarrhea of rotavirus

Bifidobacterium animalis subsp. lactis, BB-12®,

  • • Reduction if IBD symptoms
  • • Protective effect against diarrhea
  • • Reduce side effects of antibiotic treatment (antibiotic- associated diarrhea)
  • • Reduce the incidence of acute respiratory tract infections

Lactobacillus acidophilus LA5®

  • • Immune modulation
  • • Improvement of microbiota’s function
  • • Protective effect against diarrhea

Saccharomyces boulardi

  • • Prevention of diarrhea
  • • Decrease in the duration of acute gastroenteritis
  • • prevention of diarrhea of C.difficile
  • • Reduction if IBD symptoms

Bacillus clausii L. reuteri ATCC 55730

  • Anti-Helicobacter pylori effect
  • • Treatment of acute infectious diarrhea in children

Adapted from Bottazzi et al., 2007.

The duodenum tract is acidic and subject to rapid transit as well. It additionally receives pancreatic secretions and bile, thus creating a hostile environmental for microorganisms. In the duodenum, the main genera are Lactobacillus and Streptococcus and their contents are around 102 to 104 bacteria per gram. Along the jejunum and the ileum, there is a gradual increase in the bacterial number and biodiversity. Indeed, the colon contains a huge number of bacteria, corresponding to the majority of the population of the whole GI tract, achieving 1011 units per gram (ILSI Europe, 2013).

The GI tract, sterile prior to birth, is rapidly colonized during and after birth. The bacterial composition of the GI tract during and after birth depends on the environment in which the birth takes place, the type of birth (cesarean or vaginal), and the mother's microbiota. The most frequent bacterial groups include staphylococci, streptococci, corynebacteria, lactobacilli, micrococci, propionibacteria, and bifidobacteria, originated from the mother's nipples and surrounding skin as well as from the milk ducts in mammary glands (Mackie et al., 1999; Almeida et al., 2005; Solis et al., 2010). Bifidobacteria dominate the fecal microbiota of healthy breastfed infants with a corresponding reduction in facultative bacteria (Coppa et al., 2006; Oliveira et al., 2011). There a strong evidence suggesting that the early composition of neonates microbiota is important for the postnatal development of the immune system (Fooks et al., 1999; Dunne, 2001).

The human microbiota, is generally stabilized at the age of 2 to 3 years but it is influenced during the whole life by diet, disease, use of medications (particularly antibiotics) and aging. Gut microbes may be commensal or transient.

Microbes considered beneficial (Lactobacillus, Eubacterium, Bifidobacterium) usually ferment carbohydrates, do not produce toxins and may have potential benefits for the host (e.g., by interaction with immune system, competitive action against other microorganisms). On the contrary, Salmonella tiphimurium, rotavirus, some Escherichia coli types and other pathogenic microorganisms damage the host and are generally sourced by foods.

Probiotics are mainly transient although some species can be also commensal. Some, but not all, are able to replicate and persist in the gut during their intake, but they disappear after it is suspended.

Recent literature suggests that the normal microbiota is not purely a collection of bacteria but more probably is a community of different groups of microorganism that may work together for the well being of the host (ILSI Europe, 2013).

The human intestinal tract is populated by a complex association of microorganisms. The intestinal microbiota consists of two types of microorganisms: the authocthonous and the allochthonous ones, the former being resident in the gut, the latter transient with the gut content flux, taking their origin from the ingestion of food and food supplements (e.g., probiotic preparations). The authochtonous microbiota can be distinguished in “mucous” (microorganisms fixed to the intestinal ephitelium) and “lumen” (microorganisms present as free in the gut).

The main metabolic function of the intestinal microbial population is related to the fermentation of nondigestible food residues but also of the endogenous mucous secreted into the bowel by the goblet cells present in the mucosal lining. This metabolic function is represented by the fermentation of polysaccharides (resistant amylum, cellulose, hemicellulose, pectines, gums), some oligosaccharides, nonadsorbed sugars, ethyl esters, proteins, peptides, with final production of SCFA, short chain fatty acids as butyric, propionic, and acetic acid, but also of ammonia, amines, phenols, thiols, indoles.

SCFA have an important effect on the proliferation of epithelial cells, on the development and homeostasis action of the immune system. The many interactions between microbes, epithelium, and lymphoid tissue play a role in the mechanism of intestinal immunity memories (Bottazzi et al., 2007).

The colon microbiota is also implicated in the synthesis of vitamins and in the adsorption of calcium, magnesium, and iron (Bottazzi et al., 2007).

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