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How Your Gut Microbiota Affects your Immune System

Hippocrates, widely considered to be the father of western medicine, once said, "All disease begins in the gut." It turns out that he might have been right. There are around 10 trillion bacteria living inside your gut. These bacteria are collectively referred to as the “gut microbiota”. Gut bacteria play an important role in our overall wellbeing, from food digestion to regulating neurotransmitters in our brain that affect our mood. In particular, the human gut has been shown to have a key role in regulating and forming the immune system. It is estimated that 70% of your entire immune system is located there (1).

How do the gut bacteria help our immune system?

From the moment you are born, the natural bacteria in your environment can contribute to the development of your diverse and plentiful gut microbiota. This process starts from day one and continues into adult life, but early exposure to bacteria is particularly important for your gut microbiota. This early exposure helps you develop a strong immune system so that you can not only fight invading pathogens but also welcome other friendly bacteria to hitch a ride. In a nutshell, striving for a healthy gut, allows you to support your immune system and protect yourself from infection. In fact, a number of recent studies have shown that beneficial bacteria and the chemicals they release, play an important role in proliferation and differentiation of important cells in the immune system (2).

Our immune system learns from the gut

Our immune system is the link between our gut microbiota and its ability to influence health and disease. We are all born with a naïve immune system. At first, we are protected by antibodies from our mother. As our immune system develops, however, the immune cells in our body need to learn how to protect us from harm. As we get older and the support from our mother’s immune system diminishes our immune system is obliged to develop rapidly.

The gut controls inflammation

Healthy gut bacteria have an especially important role in controlling inflammation, not only in the gut itself but also in the whole body. If the intestinal barrier is not maintained, small molecules and bacteria can escape the confines of the bowel, leading to a disease referred to as “leaky gut” (3). The result of a leaky gut? The immune system is obliged to work overtime to limit the inflammation in the gut as well as fight the bacteria trying to escape the gut.


Scientists have even identified that the composition of your gut microbiome can affect the effectiveness of the seasonal flu vaccination. Unbalanced gut microbiome composition, also known as “dysbiosis”, can lead as we have already learned to inflammation. That means that if you already have an inflamed gut, your immune system is working in overdrive to protect you. That leaves precious little capacity to cope with the inflammation brought about by the flu vaccine. On the other hand, recent research has discovered that the effectiveness of the flu vaccine could be enhanced by the right kind of intestinal bacteria (4)


  1. "Allergy and the gastrointestinal system." Vighi, G., et al. (2008)
  2. "Interactions between the microbiota and the immune system." Hooper, Lora V., Dan R. Littman, and Andrew J. Macpherson. (2012
  3. "Probiotic Escherichia coli Nissle 1917 inhibits leaky gut by enhancing mucosal integrity." Ukena, Sya N., et al. (2007)
  4. "Development of the gut microbiota in infancy and its impact on health in later life." Tanaka, Masaru, and Jiro Nakayama. (2017)