The Role of Gut Flora in Health

The Role of Gut Flora in Health

role of gut flora

All disease begins in the gut.”Hippocrates. Over 2,400 years after the father of modern medicine made this claim, we are now re-discovering the role of gut flora, and just how true that statement was. The digestive tract is home to 100 trillion microorganisms, known as the gut flora.

The majority of these microorganisms are bacteria, with a small percentage consisting of fungi and protozoa. The functions of the gut flora are complex enough to resemble those of an organ, leading some researchers to refer to the gut flora as a “forgotten organ”. Indeed, the gut flora plays a number of roles so vital to the human body that if the gut were to be sterilized, long-term survival would be unlikely.

Types of Gut Flora

There are three main categories of microorganisms found in the gut:

1.)  Essential Flora: This is the “friendly” bacteria that are found in the gut. In the healthy individual, essential flora dominates and controls other types of less desirable microorganisms. When functioning normally, this type of flora is responsible for conducting numerous roles that keep the body healthy.

2.)  Opportunistic Flora: This group of microbes is found in the gut in limited numbers that are strictly controlled by the essential flora in the healthy individual. This type of flora is capable of causing disease if the essential flora becomes compromised and is unable to control the growth and numbers of opportunistic flora.

3.)  Transitional Flora: These are various microorganisms that are introduced into the body through eating and drinking.  When the essential flora is healthy and functioning normally, this type of flora will pass through the digestive tract without causing harm. However, if the essential flora is damaged, this group of microbes can cause disease.

Role of Gut Flora

Beyond controlling the population of opportunistic and transitional flora, essential gut flora plays an active role in the normal digestion and absorption of food by producing enzymes that aid in the process of breaking down proteins, carbohydrates, and fats.

It also aids in the transportation of minerals, vitamins, water, and other nutrients through the gut wall into the bloodstream for use by the body. Certain types of essential flora are capable of manufacturing nutrients such as vitamins K2, B1, B2, B3 B6, B12, folic acid, pantothenic acid, and various amino acids.

In addition to producing these nutrients to be used directly by the body, the essential flora provides nourishment to the cells of the intestinal wall that have primary responsibility for digesting and absorbing food. When the essential gut flora is compromised and not functioning normally, it is common for the individual to become malnourished and have multiple nutrient deficiencies and food intolerances. In other words, in order to remain healthy or restore health, healthy essential flora is necessary.

Immune function, lymphocyte, autoimmune conditions, gut flora

In the last decade or so, the importance of the gut flora to immune function, overall health, and disease has become an emerging area of focus.

Although there is still much to be learned about the role of gut flora in immune function, it is becoming increasingly clear that disease (and health) really does begin in the gut! Studies have shown that gut flora has a profound influence on the development and maturation of the immune system after birth (Bouskra et al., 2008; Macpherson & Harris, 2004).

In addition, it has been estimated that approximately 80-85% of the immune system is located in the gut. In a healthy individual, the essential gut flora forms a bacterial layer that covers the entire digestive tract. This bacterial layer acts as a physical barrier to protect against transitional flora, viruses, parasites, toxins, and undigested food particles.

The gut flora produces acids that lower the pH of the gut wall and make it undesirable for microbes that cause disease.

The essential flora also has the ability to neutralize many toxins and inactivate carcinogens, or substances known to cause cancer. It also plays a direct role in suppressing the processes by which cancer cells are known to develop and grow.

The essential flora has a direct effect on important immune functions because it is responsible for stimulating the tissues of the lymph system that are located in the gut wall to produce lymphocytes, a type of white blood cell that fights infections.

The lymphocytes then produce immunoglobulins, which are antibodies formed in response to contact with foreign substances (viruses, bacteria, fungi, etc). The immunoglobulins destroy and inactivate invading substances that enter the body through food and drink.

The essential flora also has a direct impact on the production and function of other many other cells of the immune system. When the essential flora is damaged, immune function is affected not only in the gut but throughout the entire body as well.

Essential gut flora plays an important role in the development of regulatory T cells, a critical component of the immune system. The types, number, and balance of regulatory T cells are directly influenced by the essential gut flora.  The dysfunction of the regulation of different types of regulatory T cells, which may result in an imbalance in certain kinds of T cells, is known to play a key role in the development of the autoimmune disease.

A broader explanation of how the gut flora influences immune function is by understanding the balance between the two arms of the adaptive immune response, known as Th1 (cell-mediated) and Th2 (humoral) immunity. In general, the role of Th1 immunity is to fight infections in the skin, mucous membranes, and cells.

When the essential flora is damaged,  the production and function of Th1 cells become impaired, allowing more invaders into the body. The body responds by overcompensating with a Th2 response, which then predisposes the individual to allergic-type reactions, chronic inflammation, and autoimmunity. Healthy essential gut flora is the key to keeping these arms of the adaptive immune system in balance, thus preventing disease.

Maintaining Healthy Gut Flora

Fermented Sauerkraut

There are many contributing factors to damaged and imbalanced gut flora, including a poor diet high in refined carbohydrates, chronic stress, the use of certain medications, such as antibiotics, non-steroidal anti-inflammatory drugs (NSAIDs), and oral contraceptives, cesarean section birth, bottle feeding, and toxic exposure to various chemical substances.

While you may have no control over some of these factors (whether or not you were bottle-fed, for example), there are steps you can take to support your essential gut flora.

A Paleo lifestyle that eliminates processed foods and refined carbohydrates, adds an appropriate level of exercise and rest, and seeks to manage stress effectively will go far in maintaining a healthy balance of bacteria in the gut.

The consumption of probiotic-rich foods and drinks, such as sauerkraut and other fermented vegetables, kombucha tea, water kefir, and coconut milk yogurt, can also help to contribute to healthy gut flora.

What steps have you taken to maintain healthy gut flora?


Bouskra D. et al. (2008). Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature 456(7221), 507–510.

Campbell-McBride, N. (2010). Gut and psychology syndrome. Cambridge, United Kingdom: Medinform.

Kosiewicz, M.M., Zirnheld, A.L., & Alard, P. (2011). Gut microbiota, immunity, and disease: A complex relationship. Frontiers in Microbiology, 2(180).

Macpherson, A.J. & Harris, N.L. (2004). Interactions between commensal intestinal bacteria and the immune system. Nature Reviews: Immunology, 4(6), 478 – 485.

Wu, H. & Wu, E. (2012). The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes, 3(1), 4 – 13.




16 Responses

  1. How do you feel about fecal transplants? Are they something worth looking into if someone is experiencing persistent leaky gut and/or gut dysbiosis?

    • I’m a huge advocate of fecal transplants. The conventional medical community recognizes that fecal transplants help with C. diff infections, but I think that their application is much broader than that. I believe they can also help tremendously in cases of severe gut dysbiosis and possibly in all types of autoimmune disease. This is definitely an area that should be a focus of research and exploration in the health care community, but it isn’t getting nearly the attention it deserves, which is why many patients are resorting to doing the procedure on their own.

  2. I had ulcerative colitis for 3 years then went on the Specific Carbohydrate Diet. I began getting better slowly. I did a home fecal transplant and my symptoms went away without drugs to suppress my immune system. I stayed eating SCD for 8 months then had some bread over a week’s time and my UC symptoms came back. I did another home FMT and within a week I was better. I guess all the back bacteria in my gut have not all died. I feel great – no sugar, starch, grains, lactose or yeast. I eat lot of fresh and cooked fruits and veggies and meat. I also make homemade yogurt and kefir (these are lactose free) and fermented foods. No drugs and no symptoms – worth the change.

    • That’s fantastic. I did a home fecal transplant myself and I started seeing a huge change within a week! Some people are disgusted when I tell them, but truly I do not care. It probably saved my sanity after dealing with persistent gut dysbiosis for 4 years.

    • That is so wonderful to hear that the fecal transplant worked well for you! I think fecal transplants have great potential for people with inflammatory bowel disease–and how wonderful not to have to take toxic medications with horrendous side effects.

  3. Great article. Gut is fascinating to me. Lately, I’ve focused on prebiotics, since I think they are more potent in stimulating our growth of friendly gut bacteria than probiotics. In fact, for the past 2 months, I’ve been consuming over 1 pound (raw weight) of onions a day. Yes, over a pound a day! I just lightly cook them in water and have with lean ground beef or shrimp. This is a healthy and tasty way to get in a lot of prebiotics during the day.

    I am thankful I’m not very low carb because I eat a lot of gut friendly soluble fibers from onions, pumpkin, and potatoes.

    • Hi Kate! I think that both prebiotics (found in soluble fiber) and probiotics are both important to gut health. I tend to believe that adequate prebiotics can be consumed by eating a balanced Paleo diet that contains a variety of fresh vegetables. Onions are a great source of prebiotics, although I don’t think it’s necessary to eat as much of them as you are in order to get enough (although it’s certainly not going to hurt you as long as you can tolerate it). You’re correct that someone who follows a Paleo diet that is carb-restricted may have difficulty getting enough prebiotics, but in general, I don’t think it’s necessary to supplement prebiotics. It’s great that you are getting your prebiotics through the food you are eating!

  4. I am doing GAPS and so use fermented dairy. I mainly use cultured cream as I lead more towards the slow evacuation side. I notice that after I eat cream, I get some brain fog and low energy and am worried this is a sign of some type of sensitivity although the practitioner who I consulted with says cultured cream has almost no casein. What are your thoughts on healing the gut without cultured dairy as GAPS does? I am considering taking it out to see how I feel but do not want to thwart my effort at healing because I know how important it is to keep the good flora coming because the goal is to repopulate. Thanks!

    • I have some personal experience with this as I first started my own healing diet journey with GAPS. I did not do well with the fermented dairy and it wasn’t until I removed all dairy that I started to make significant progress. It is true that fermented dairy should have almost no casein or lactose, but it’s possible that you are just sensitive to dairy in general. People can develop intolerances to all sorts of food when they are in a leaky gut situation. I’ve had clients that are sensitive to things like lettuce or bananas, so it just really depends. Another thing to consider would be a histamine intolerance, as fermented dairy is a high histamine food. As far as thwarting your healing, you can incorporate fermented vegetables or other fermented foods instead of the cultured dairy. I often put clients on a modified GAPS diet without the dairy because it is problematic for many.

      • Hi Katy,

        I appreciate your response.

        I think you are right about possibly being sensitive to dairy even though there is little casein or lactose. Since I use cultured cream (have found kefir causes constipation), there is said to be almost no casein there but the fact that I get brain fog and low energy after eating it is a sign to me so I think eliminating it for a time being makes sense.From what I understand, there are certain species of bacteria in the dairy that we cannot otherwise get from fermented veggies and so I often wonder if the dairy is necessary to some extent. I also wonder if coconut water kefir would offer the same benefit and therefore be used instead.

        I had my histamine checked a couple years ago and it was normal. Is this an ok way to determine I don’t have histamine problems?

        You mentioned you eliminated dairy, can you tell me what difference you noticed?

        • Histamine intolerance is a complex condition and I don’t believe blood testing to be that accurate. Conventional medicine sets a “normal” level of histamine in the blood, but everyone has their own unique histamine tolerance threshold. Histamine intolerance is definitely related to dysbiosis of the gut.

          I was struggling with some serious digestive issues at the time that I was on the GAPS diet. It wasn’t until I eliminated the dairy and made some other changes in the GAPS protocol that the diarrhea stopped completely. There are different species of bacteria in the fermented dairy, but you have to look at the bigger picture. Your gut is not going to heal if you are sensitive to dairy and you continue to consume it. Another option would be a high quality probiotic.

  5. Hi Katy.
    I listened to the podcast of Karen Pendergrass about her Fecal transplant. I have been a sufferer of several guts problems for years & would be gratefull about more info on how to go for a homemade one.

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