Gut Microbiota


Gut microbiota refers to communities (colonies) of microorganisms that live in the human gastrointestinal tract (gut). The large intestine has by far the largest numbers of microbe communities. The resident microorganisms include many types of bacteria, viruses, archaea, and eukaryotic microbes. Five of the dominant bacterial phylotypes found in cultures of stool samples are Bacteroides vulgatus, Eubacterium rectale, E. prausnitzii, Collinsella aerofaciens, and Ruminococcus bromii. The distinct combinations of bacteria in the gut are specific to each person who serves as a host, referred to as host-specific organisms or enterotypes. Microbes found in regions of the gastrointestinal tract and in organs throughout the body are referred to collectively as the human microbiota, or simply the microbiome. Sometimes the gut microbiota is referred to as intestinal flora.


Illustration of the relationship between an imbalance in intestinal flora and autism.

Illustration of the relationship between an imbalance in intestinal flora and autism. An imbalance between good bacteria in intestinal flora (lactobacilli) and bad bacteria (Clostridium and Desulfovibrio) that produce neurotoxic molecules that flow to the brain through blood vessels leads to behavioral and autistic disorders.
(BSIP/JACOPIN/Medical Images)


The human gastrointestinal tract extends from the mouth and esophagus through the stomach and intestines to the rectum. It is colonized by communities of different microorganisms known collectively as the gut microbiota. More than 100 trillion different microorganisms live within the human body, including bacteria, viruses, and nonbacterial prokaryotic and eukaryotic microbes. At least 1,000 species of bacteria are found in humans, comprising 150 times more microbial genes than in the whole human genome. Host-specific gut microbiota evolve through the individual's lifetime and can change based on dietary and environmental influences. An individual's nutritional status, behavior, and stress levels may alter the composition of the gut microbiota, and the reverse is also true—the gut microbiota may affect the individual's physical and mental or emotional health. The particular gut microbiota in one individual can be either beneficial or detrimental to the individual's overall health status. The assortment of organisms in the gut can be a contributing cause of disease because the presence or absence of certain organisms may affect the functioning of body organ systems and be a source of inflammation and infection. A balanced composition of gut microbiota is necessary so that there is no overgrowth of a specific type of bacteria and no absence of beneficial bacteria considered essential in maintaining the health and proper functioning of the digestive system.

Gastrointestinal disorders are common among the general population and many are influenced by the composition of the gut microbiota. Disruption of the gut microbiota (dysbiosis) is often accompanied by overgrowth of a harmful (pathogenic) bacteria or fungi due to significant loss of microbial diversity. Such alterations in the gut microbiota composition may produce symptoms such as abdominal distension, abdominal pain or cramping, headache, dizziness, and loss of appetite. The symptoms may or may not be associated with a specific disease or disorder, but will often have a significant impact on an individual's quality of life. A range of common gut-related disorders and intestinal diseases that are linked to alterations in the composition of the gut microbiota include:

Many chronic diseases are also associated with the human microbiota, including obesity, diabetes mellitus, metabolic syndrome, atherosclerosis, autoimmune diseases (e.g., rheumatoid arthritis, fibromyalgia, lupus erythematosus), alcoholic liver disease, nonalcoholic fatty liver disease, cirrhosis of the liver, and liver cancer (hepatocellular carcinoma).

Diet and the gut microbiota

The diet can have major short- and long-term influence on the composition of the gut microbiota. Because the colonies of microorganisms differ between individuals, the responses of individuals to diet and dietary changes will also be different. The complex interaction between the gut microbiota and dietary factors has a direct affect on health. A balance must be achieved between defending the body against the constant threat of infection from organisms in the intestinal tract versus the beneficial effects of nutrient processing and immunity provided by other organisms living in the gut.

Different dietary patterns provide a range of factors that either promote the growth of specific bacterial phylotypes or inhibit their growth. Food components in the diet (mainly fiber) that cannot be digested by enzymes form a base, or substrate, for microbial metabolism in the gut. Most microbial metabolism takes place in the large intestine where the gut microbiota ferments carbohydrates and proteins that escaped absorption in the small intestine. The stomach and small intestine have relatively lower numbers of microorganisms compared to the large intestine, which has an exceptionally dense microbe population. Two bacterial families (phyla) account for the majority of bacteria in the large intestine: gram-negative Bacteroidetes and Firmicutes. The Bacteroidetes phylum includes Bacteroides and Prevotella, which are the major producers of propionate (propionic acid), one of the main shortchain fatty acids. Firmicutes are the main producers of the short-chain fatty acid butyrate (butyric acid), which is essential to human health. These include Actinobacteria, Proteobacteria (including Escherichia coli) and Verrucomicrobia, bacteria whose presence also influences health outcomes. Organisms in the large intestine acquire energy from fermentation of nondigested dietary carbohydrates and secretions by the host, forming short-chain fatty acids, gases such as carbon dioxide and hydrogen, and vitamins—all essential to having a healthy gut microbiota and overall good health.

Prokaryotic microbes that have no cell nucleus or membrane-bound organelles in their cells.
Disruption of the gut microbiota.
The overall composition of the gut microbiota, including all organisms.
Eukaryotic microbes—
Nonbacterial single-celled microbes such as algae, protozoa, and fungi.
Human genome—
A complete set of nucleic acid sequences encoded as DNA in humans.
Microbial genes—
The genetics of microbial species, including genotypes of bacteria, archaea, viruses, and some fungi.
An environmental DNA sequence used to classify organisms.
Pseudomembranous colitis—
Inflammation of the colon associated with overgrowth of the bacterium Clostridium. Also called C. difficile colitis.
Short-chain fatty acids (SCFA)—
Produced in the large intestine by the gut microbiota, SCFA help determine the gut environment, support colon function, and provide cellular energy for the host and microbes in the gut.

The effects of dietary patterns are studied by examining stool samples to identify the distribution of organisms in the gut microbiota and whether it is beneficial or detrimental to the health status of the individual. Various types of diets affect the composition of the gut microbiota differently, including:

Intestinal environment

The diet is a key factor in determining the internal environment of the gastrointestinal tract, especially that of the stomach and intestines. Dietary patterns are linked to the distinct combinations of bacteria, or enterotypes, in every individual. Bacteria in the large intestine ferment soluble fiber from the diet, producing small amounts of energy and short-chain fatty acids. The fatty acid butyrate helps reduce inflammation in the intestinal mucosa and protects the gastrointestinal barrier, keeping nutrients in and unwanted bacteria and other organisms out. In turn, the colonic environment has a strong influence on the composition of the gut microbiota, particularly the intestinal pH (percentage hydrogen, a measure of acid/alkaline balance), oxygen level, and bile acid levels. A low pH (6.0) is more acidic, 7.0 is neutral, and a higher pH (greater than 7.0) is more alkaline. The colonic environment varies from mildly acidic to more neutral or a relative acid/base balance. Many bacteria grow rapidly in an acid environment, but growth of Bacteroides, for example, is slowed in an acid environment. A slightly alkaline environment (about 7.4, but no higher) may help to reduce numbers of organisms in established colonies, which can effectively correct bacterial overgrowth. Eating abundant green vegetables, especially dark green leafy vegetables, such as kale, collards, broccoli, and spinach, helps to maintain a slightly alkaline environment.

Bile acids derived from cholesterol produced in the liver are necessary in the intestines for their antimicrobial activity. Bile acids secreted into the small intestine can cause a major favorable shift in the gut microbiota composition. In the large intestine, however, bile acids are modified by the gut microbiota and can become cancer-causing (carcinogenic) secondary bile acids.


Foods, medications, antibiotics, and vaccines can disrupt the gut microbiota. If these sources cause shifts in the composition of the microbial communities, the immune system response of the individual may be affected negatively. The microbial composition modulates the host's immune response and controls the possible growth of harmful pathogenic species. In infants, for example, antibiotic use changes the gut microbiota and may have a negative effect on the development of the immune system, sometimes leading to greater susceptibility to allergies, asthma, and other conditions in later life.

Prenatal maternal exposure to bacterial species appears to influence early infant immune response. Exposure of the mother to microbes during pregnancy (prenatal exposure) is believed to be important in supporting optimum immune functioning of the mother and the newborn after delivery. For example, mothers who visited farms and farm animals were found to be unlikely to have children with allergies. This type of exposure is thought to help the infant develop a diverse gut microbiota and thereby reduce allergic responses. Conversely, women whose amniotic fluid, which is usually sterile, was found to contain bacterial species, were shown to have increased levels of pro-inflammatory cytokines (e.g., interleukin-6) and were more likely to have a newborn with systemic infection (sepsis). The mother, as host for microbial communities, must balance the beneficial bacteria in the gut microbiota with protection against overgrowth of invasive disease-causing species.

See also Constipation ; Crohn's disease ; Ulcers .




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Academy of Nutrition and Dietetics, 120 S. Riverside Plaza, Ste. 2190, Chicago, IL, 60606-6995, (312) 899-0040, (800) 877-1600,, .

Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., HFS-009, College Park, MD, 20740-3835, (888) 723-3366, .

International Foundation for Functional Gastrointestinal Disorders, PO Box 170864, Milwaukee, WI, 53217-8076, (414) 964-1799, (888) 964-2001, Fax: (414) 964-7176,, .

National Digestive Diseases Information Clearinghouse (NDDIC), 2 Information Way, Bethesda, MD, 20892-3570, (800) 891-5389, TTY: (866) 569-1162, Fax: (703) 738-4929,, .

U.S. Department of Agriculture, 1400 Independence Ave. SW, Washington, DC, 20250, (202) 720-2791, .

L. Lee Culvert

  This information is not a tool for self-diagnosis or a substitute for professional care.