Bacteria and other microorganisms live inside the gastrointestinal tract (digestive system) of animals, including humans. Majority of these bacteria are found in the intestine, mainly the large intestine, while some have also been found to be residing inside our mouth. This gut flora is established at one or two years of age after birth and has a mutualistic association with the cells of intestine, rather than invasive. Humans provide these microbes with the shelter and protection while the bacteria in turn synthesize useful products such as vitamin B and vitamin K.


Stomach Flora

Stomach has high acidity due to the secretion of hydrochloric acid. Also certain hormones that hydrolyze the proteins. Consequently, majority of the bacteria are absent. But some species of Lactobacillus, Staphylococcus and Streptococcus are still present. Some species of cancer and ulcer causing bacteria may develop on the internal lining of stomach, mainly including Helicobacter Pylori.

Flora of Small Intestine

Trace amounts of microorganisms are present in the distal portion of small intestine while greater number of these microbes reside inside the large intestine. Alkaline environment of small intestine supports the Enterobacteriacae. Other organisms such as fungi and protist also make up the gut flora but their activities are still unknown. Imbalances or destruction to these gut flora may cause certain malfunctioning to human body such as obesity. But some species are thought to be causing diseases, infections and even cancer, in some situations.


The gut flora performs some of the major functions in the human body which include: fighting against the invading pathogens, helps the intestinal walls to develop, digesting the indigestible components of food, help to establish immunity and synthesize some significant compounds used in the production of macromolecules.

The gut flora ensure that any invading organism does not take hold of the space and shelter. In order to do so, they utilize all the available space and nutrients. They are also capable of secreting the compounds that would kill or otherwise stop the growth of conquering organisms. Disruption of this normal flora causes the development of microbes that would cause diseases and infections.

Formation of GALT

In humans, the gut flora develops after one or two years of birth. During this process, as the flora establishes in the intestines of the infants, the walls of the intestine also begin to grow. Thickening and helping the flora to multiply and gain number. Additionally, Gut-associated Lymphoid Tissue (GALT) is also formed in the walls of intestine. GALT can distinguish between the normal flora and other types of species. It is also tolerable to the digestible nutrients and other compounds.

Immune Response

This gut flora helps to stimulate an immune response. By the production of anti-inflammatory compounds called cytokines While it also triggers, the release of antibodies. This flora causes the B cells of the immune system to develop into IgA. IgA is an important antibody that works in the digestive tract of the humans. As it helps to destroy the bacteria that causes inflammation. In this way, IgA maintain a healthy environment. In another method, the gut flora ferments certain substances in the intestine and produces Short Chain Fatty Acids (SCFA). These SCFA in turn stimulate some immune cells which help to slow down the infection.

Gut flora role in Metabolism

Gut flora plays a major role in the metabolism and digestion of various components of food. Many bacteria possess the enzymes for the digestion of carbohydrates such as starch, oligosaccharides and sugars, which the human beings lack. Without this gut flora, humans would be unable to extract nutrients from these carbohydrates. The sugars that are hydrolyzed by gut microbiota are further fermented to produce substances such as propionic acid and lactic acid. Which act as a source of energy for the bacteria itself, while the breakdown of acetic acid can provide energy to the gut cells too.

This gastrointestinal microbiota also helps in synthesizing vitamins and even in the absorption of elements such as calcium and magnesium. One type of bacteria called Methanobrevibacter smithii functions to produce methane inside the guts of humans. In addition to digesting food remains, microbiota can also break down certain drugs and food toxins. More than 30 drugs have been known to be metabolized by gut bacteria, either by complete breakdown or by inactivation.

Destruction of Gut Microbiota

The population of gut flora maybe effected by number of factors. Such as antibiotic abuse, drug abuse, severe infections and immune compromise. Overuse or misuse of antibiotics may lead to the death of microbiota. Which would lead to the difficulty in digestion of useful substances in food. Apart from illness, the number of microbiota also decreases in cases of pregnancy. Researchers have also found that pharma biotics and other pharmaceutical formulations may affect the efficiency of these bacteria causing diarrhea or even constipation.


Studies suggest that gut microbiota may be involved in causing cancer and inflammation outside the parts of gastrointestinal tracts. Tumor production is associated with gut flora from direct or indirect routes. Direct pathway involves the residence of microorganisms in the walls of other organs. Indirect pathway involves the production of some chemicals that act as carcinogens. In response to other microbes or to compounds in result of digestion, for example bile acids and steroid hormones. As some species cause cancer, some other organisms such as Lactobacillus and Bifidobacterium may be involved in the prevention of cancer.


Some members of gut flora such as Helicobacter pylori is found to cause stomach ulcer. When they reside in the walls of stomach, they stimulate the Hydrochloric acid producing cells to release more HCl. More production of acid and less release of mucus causes the destruction of stomach walls, a condition called “Ulcer”.

Not only mammals possess these flora, but it also has been found that some insects  have these type of bacteria. Which perform many important tasks.

By Razmia Sabahat Butt

I'm a student of BS Applied Biosciences at NUST, Islamabad.