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Gastro Intestinal Flora and Our Health
May 1, 2016

The systems of the human body are created with a staggering degree of perfection. The body has approximately 1013 cells at any given time, and these ensure that our systems run flawlessly, without us ever thinking about it. Inside our body, there are also 1014 microorganisms. These microorganisms do not harm our body, and some even benefit us. They’re known as the body’s flora.

An unexpected increase in flora, which is normally necessary for a healthy life, can pave the way for diseases. There are, on average, 200 grams of bacteria on an adult’s skin, 20 grams in the mouth, and 20 grams in the lungs. The gastrointestinal tract contains a dramatic amount of flora – 1.5 kg of bacteria – this equals 100 trillion organisms. This flora covers the intestinal mucosa, which is an area of approximately 300 m2. This functions as a protective layer, and is of vital significance.

Since some 90% of the microorganisms inside us are dependent on the human body to survive, their relationship with us is symbiotic. Most of this flora improves our immune system. Our body tolerates the beneficial bacteria in the flora, and it fights against the harmful organisms.

Much of our flora develops before we’re born. Since a baby is sterile prior to birth, it receives some 100 types of microorganisms from the birth tract and environment, which start building the body’s flora. Factors such as the type of delivery (natural or caesarian), the mother’s age, the baby’s health, the type of nutrition (mother’s milk and baby food), and the mother’s food intake play a determining role in the types and amount of the microorganisms that make up the flora. Babies born in the natural way have a stronger immunity than those born through caesarian sections, thanks to the flora they gain from their mother.

While nearly 700 types of microorganisms inhabit the body of a 6 month old baby, a person has a fully developed system of flora at 3 years of age.

Flora in the digestive track

The digestive track is where food and nutrients are refined for our body’s benefit. Our GI tract is about 250-400 meters in area, comparable to a tennis court. It has the second largest surface area in the body. About 60 tons of food pass through a person’s digestive track over his or her lifetime.

The part that contains the most diverse microorganisms is the mouth. Conversely, the floral density of the esophagus is low. Microorganisms that come by means of saliva and foods are found here. As the interior of the stomach is highly acidic (pH: 2), the number of microorganisms in the stomach is quite low (10thousand/per ml).

Considering the amounts of bacteria in an average adult body, one milliliter of the duodenum has ten thousand bacteria; the beginning of the small intestine has a hundred thousand, its ending has a hundred million, and the colon has about a hundred billion to a trillion microorganisms. The intestines of healthy individuals have nearly 500 different bacteria species.  The fact that trillions of organisms are found in the human body may sound a bit frightening, but 98% of them are beneficial.

The forgotten organ

The intestinal flora, which is indispensable for a healthy life and is specific to every person, is also referred to as “the forgotten organ,” since its metabolic activity is rather high.

Substances such as amino acids, vitamins, and antioxidants, found in the content reaching the large intestine, are metabolized by the intestinal flora and thus the needs of intestinal cells are met. These bacteria have the duty to stimulate cell division and prevent the reproduction of harmful bacteria, toxic substances’ passing from the guts to the bloodstream, and the emergence of skin diseases. Most of the time, we are not even aware of the presence of these marvelous helpers.

The intestinal flora stimulates the lymph tissues around it and triggers an antidote against germs. The fact that the lymphoid structure did not develop in experimental animals bred in a bacteria-free environment indicates how crucial microorganisms are for the immune system.

The spoiling of the intestinal flora can cause problems like diarrhea, constipation, gas, allergies, infection, high cholesterol, headaches, and fatigue. The toxins of the disease-causing germs damage the intestinal membrane and increase its permeability. Thus, toxins join the bloodstream and they might reach as far as the brain. These toxins can influence brain functions, and lead to problems with sight and balance, fatigue, and amnesia, as well as leading to sleep disturbances, and pains in the muscles and joints. These toxins also hinder the absorption of nutrients and can cause malnutrition.

In order to keep the intestinal flora balanced, it is necessary to keep away from antibiotics, carbonated beverages, refined food, and alcohol.  Eating various kinds of food during the same meal may cause difficulty for the digestive system and the flora. Fruits eaten at night burden the digestive system, causing irregularity in the flora and the formation of gas. For this reason, it is wiser to eat fruit half an hour before, or two hours after, a meal.

Our probiotic friends

Probiotics are beneficial microorganisms that balance the intestinal flora. Probiotic products are foods with added beneficial microorganisms. As the microorganisms in normal flora turn carbohydrates into the suitable form to be used by the body, they are known as friendly bacteria. These microorganisms, which form 95% of the flora in little infants, synthesize certain vitamins, and protect the baby against some diseases.

Fermented foods, such as yogurt, cheese, kefir, olives, vinegar, naturally fermented pickles, and sourdough bread, enrich the intestinal flora. However, increasing foods’ shelf life with methods as UHT or pasteurization can negatively affect the intestinal flora.

Probiotic bacteria are resistant to stomach acid, bile salt, and lysozyme. They produce antimicrobial substances such as lactic acid, acetic acid, and bacteriocin to prevent the proliferation of undesirable microorganisms in the intestine. In addition, they form a protective layer on the intestinal walls against toxic substances.

Antibiotics, alcohol, junk food, stress, a poor diet, and intestinal surgeries can all lessen the amount of probiotic bacteria in the gut.

Today, probiotic capsules with differing benefits are on the market. A diet rich in natural foods such as vegetables, fruits, meat, and eggs, along with probiotic foods such as yogurt, are good for the intestinal flora. It is thought that some diseases which cannot be treated could perhaps be cured with probiotics.

The intestines and our health

During the development of the embryo, some of the same groups of cells are used for forming the brain and the digestive system. These structures are in constant communication with the vagus nerve.

There are 100 million nerve cells in the structure of the intestines. After the brain, the intestines have the highest amount of nerve cells in the body. As such, the digestive tract plays a big role in determining a person’s mood. The toxins it secretes can cause a person to feel bad. This is why some scientists humorously say that we have a second brain in our belly. Some states of worry, excitement, and emotional intensity have corresponding gut pains. There is more of the hormone serotonin, which balances a person’s mood, in the intestines than in the brain. When there is a pain in the body, benzodiazepine – a pain-alleviating substance used in anti-depressants – is produced by the intestines. This is why the intestines work faster in times of pain.

Some of the different bacteria in the intestines need sugary nutrients and others need oily nutrients. In order to obtain these nutrients, bacteria send signals to the secretive glands and nervous system, and make the person feel like consuming certain foods.

A person needs healthy intestines to lead a healthy life – they need balanced flora for healthy intestines. New food technologies in the last century, changes in dietary habits, chemical pollutants, antibiotics used in agriculture, and other chemical substances in food and beverages, have all upset the balance of the digestive track’s flora. This imbalance is causing an increase of related diseases. In order to reduce these diseases, our body needs more of its old, friendly bacteria.


  • Berg RD. The indigenous gastrointestinal microflora. TrendsMicrobiol 1996; 4:430-435.
  • de Vrese M, Schrezenmeir J. Probiotics, prebiotics and synbiotics. AdvBiochemEngBiotechnol. 2008;1111:1-66.
  • Macfarlane GT andCummings JH: Probiotics and prebiotics: can regulating the activities of intestinal bacteria benefit health? BrMed J. 318:999-1003,1999
  • O’Sullivan GC, Kelly P, O’Halloran S. Probiotics: an emerging therapy. Curr Pharm Des 2005; 11: 3-10.
  • Penner R, Fedorak RN, Madsen KL. Probiotics and nutreceuticals: non-medicinal treatments of gastrointestinal diseases. Curr Opin Pharmacol 2005; 5: 1-8.
  • Sathyabama S, Khan N, Agrewala JN. Friendly pathogens; preventor provoke autoimmunity. CritRevMicrobiol. 2014;40:273-80.
  • Tannock GW. Can the gut microflora of infants be modified by giving probiotics to mothers? J Pediatr Gastroenterol Nutr 2004; 38: 244-246.