What is Gut Flora (Gut Microbiota)?


Gut flora, or microflora, refers to microorganisms that occur naturally in the digestive tract of animals and humans. Microbiota, the bacteria which reside in the gut flora can be either

  • good : protective agents that strengthen the immune system OR
  • bad : destructive agents that weaken the body.

Bad microbiota or bacteria produce toxic by-products that cause long-term illness and chronic degeneration of the body.

Good microbiota or bacteria, that make up most of the flora in the gut and colon, can favourably alter the intestinal flora balance to positively impact our health via the following functions:

Inhibit bacteriaBreak down foodMetabolize toxinSythesize vitamin

Inhibit bacteria, Metabolize toxin, Break down food & Sythesize vitamin

  1. Metabolic function, carbohydrate fermentation and absorption

    1. digest our food and produce enzymes that can metabolize protein into absorbable amino acids. These key enzymes also transport key vitamins, minerals and other nutrients through the intestinal wall and into the blood stream where they are effectively carried to cells that are in need of these nutrient packages.
    2. contain enzymes which human body lack for breaking down certain polysaccharides (e.g. sugar-like lactose for those who are lactose intolerant, and sugar alcohols).
    3. ferment carbohydrates into short chain fatty acids (SCFAs), and SCFAs can improve the absorption of essential dietary minerals such as calcium, magnesium and iron.
    4. Bad bacteria break down proteins like enzymes, dead host and bacterial cells, and collagen and elastin found in food, and produce toxins and carcinogens. But good bacteria produce vitamin K2, B1, B2, B3, B6, B12, folic acid and pantothenic acid instead. Without adequate microflora production, the body will suffer from poor calcium metabolism, neuromuscular function and chronic inflammatory conditions due to deficiencies in these very important nutrients.
    5. produce gases and organic acids which enhance the absorption and storage of lipids.
    6. metabolize dietary carcinogens. Heterocyclic amines (HCAs), which are produced by cooking food such as meat and fish at high temperatures, can induce tumors in organs like the breast, colon and prostate. HCAs are naturally occurring; therefore, the complete avoidance of them is impractical. But the metabolic function of gut flora can help to lower the risk of such tumors that are difficult to avoid. The same applies to excessive intake of fat and sodium chloride, which can later promote tumor.

  3. Repression of pathogenic (infectious) microbial growth

    • Good bacteria produce lactic acid and different fatty acids during fermentation, and these organic acids lower the pH in the colon, which can inhibit harmful bacteria growth and infection.
    • Good bacteria prevent some harmful bacteria species from colonizing the gut through competitive exclusion, an activity termed the “barrier effect“. Harmful yeasts and bacterial species are unable to grow excessively due to competition from helpful gut flora species adhering to the mucosal lining of the intestine, thus animals without gut flora are infected very easily. The barrier effect protects humans from both invading species and species normally present in the gut at low numbers, whose growth is usually inhibited by the gut flora.
    • Good bacteria prevent the growth of harmful species by competing for nutrition and attachment sites to the mucosal lining of the colon. Indigenous gut floras also produce bacteriocins, an anti-bacteria substance that inhibit growth of similar bacterial strains, substances that kill harmful microbes and the levels of which can be regulated by enzymes produced by the host.

    Indigenous bacteria refer to bacteria that were inborn or that were originally growing and living naturally in the digestive tract.


  5. Immunity

    • Bacteria promote the early development of the gut’s mucosal immune system. The immune system recognizes and fights harmful bacteria, but leaves the helpful species alone, a tolerance developed in infancy. As soon as an infant is born, bacteria begin colonizing its digestive tract. The first bacteria to settle in are able to affect the immune response, making it more favorable to their own survival and less so to competing species; thus the first bacteria to colonize the gut are important in determining the person’s lifelong gut flora makeup.
    • Good bacteria provide resistance against infection and even bad bacteria, if exposure to very small amount can help to train the immune system to develop antibodies.

  7. Preventing allergy

    • Gut flora affects a person resistance to allergies, an overreaction of the immune system to non-harmful antigens. Infants and young children who have allergies usually have higher chances of having the harmful species C. difficile and S. aureus, and lower prevalence of good bacteria such as Bifidobacteria. Good bacteria stimulate the immune system and “train” it to respond properly to antigens. A lack of these bacteria in early life leads to an inadequately trained immune system that overreacts to antigens.

  9. Preventing inflammatory bowel disease (IBD)

    • Good bacteria ferment carbohydrates into short chain fatty acids (SCFAs) and SCFAs can inhibit harmful bacteria growth, thus lowering the chance of inflammatory bowel disease (IBD), which is a condition related to the inflammation of the intestinal wall and lining, causing diarrhea.


A healthy and balanced gut flora is the basis of a proper digestive system. If you have a flourishing intestinal colony of beneficial bacteria, you are better equipped to fight the growth of disease-causing bacteria.

A pathogen or infectious agent (colloquially known as a germ) is a microorganism, in the widest sense, such as a virus, bacterium, prion, or fungus, that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.

Pathogenic – means disease forming.