Bacteria That Inhabit The Human Gut

The estimated number of bacteria carried by each healthy human mainly in the gut is 1014, a figure outnumbering body cells by ten to one. Such population sizes remain gigantic even after accounting for the fact that these bacteria belong to multiple species. Several hundred species have been found on the skin, and there have been estimates of up to 1000 species in the human gut.2

The bacterial inhabitants of the human gastrointestinal tract constitute a complex ecosystem. Anaerobic bacteria predominate. The upper gastrointestinal tract (the stomach and upper intestine) normally contains a sparse microflora; most of these organisms are derived from the mouth/throat and pass through the gut with each meal. Colonization of the upper intestine by colilform organisms is an abnormal event and is characteristic of certain infectious pathogens such as Vibrio cholerae and E. coli. In contrast, the large intestine normally contains a luxuriant microflora with total concentrations of 1011 bacteria/g of stool. Anaerobes such as Bacteroides, anaerobic streptococci and Clostridia outnumber facultative anaerobes such as E. coli by a factor of 1,000. Penetration of bacteria through the mucosal surface of the intestine is an abnormal event; pathogens such as Shigella, Salmonella and Campylobacter invade in this way.

Pathogenic Campylobacter invades the human body by penetrating through the surface of the intestine.
Source: CDC/ James Archer

The same mechanisms that control the normal flora also protect the bowel from invasion by pathogens. Gastric acid in the stomach kills most organisms that are swallowed. Individuals with reduced or absent gastric acid have a high incidence of bacterial colonization in the upper small bowel and are more susceptible to bacterial diarrheal disease. Bile has antibacterial properties and thus may be another factor in controlling the flora. Forward propulsive motility (peristalsis) is a key element in suppressing the flora of the upper bowel. Finally, the microflora itself, by producing its own antibacterial substances (e.g., bacteriocins and fatty acids), stabilizes the normal populations and prevents implantation of pathogens.

Human Gut Bacteria Linked To Obesity

There are two predominant bacterial groups in the human GI tract, Bacteroidetes and Firmicutes. Recent research has discovered a relationship between the balance of these groups and obesity. Firmicutes bacteria, which include Bacillus, Clostridium, and Lactobacillus species, are very efficient in metabolizing plant polysaccharides into monosaccharides and short-chain fatty acids. These can then be absorbed and converted to more complex lipids (fats) in the liver. The Bacteroidetes group, which includes Bacteroides and Prevotella species, are not as efficient and can contribute to a significant accumulation of fat stores in the body.3

Human Gut Bacteria Linked To Type 1 Diabetes

Type 1 diabetes (T1D) is an autoimmune disorder typically developing within the first 5–6 years of life, beginning with inflammation of the pancreas, progression to autoimmunity and ultimately destruction of insulin-producing beta cells in the pancreas, resulting in dependence on daily exogenous insulin to control blood glucose levels. T1D is a complex disorder whose causes are poorly understood, but it is widely believed that a combination of genetic and environmental factors such as the type of gut bacteria contribute to increased T1D risk. Bacteroides dorei has been implicated in the development of T1D autoimmunity in children at high risk for the disease.3


  1. Medical Microbiology. The University of Texas Medical Branch at Galveston
  2. Laboratory Evaluations for Integrative and Functional Medicine By Richard S Lord, Richard S. Lord and J. Alexander Bralley
  3. Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes



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