How Does Gut Health Impact Your Immune System?

You probably know that you have a large population of microbes living in your gut. This microbiome made up of bacteria, fungi, and viruses plays a vital role in your state of health. There may be as many as 1,000 different strains of microbes in your gut at any one time. As well as your digestion, research suggests that the gut microbiome may influence many aspects of your overall well-being. One system that seems to be affected by gut health is your immune system.


We usually think of bacteria as being dangerous or at least unpleasant. Bacteria can cause serious illnesses, after all. While some of the bacteria and other microflora in your gut are indeed pathogenic, many of them are beneficial. Indeed, some bacteria are vital to your health. Throughout your life, from birth onwards, your microbiome works with your body. As an infant, it helps you to digest milk. Later, your microbiome breaks down indigestible fiber so that your body can take up the nutrients from it. Your microbiome produces vitamins and helps to regulate many of your body’s systems. In particular, your gut health and immune system seem to be closely related.

Immune system & gut microbiome connection

Does the immune system start in the gut? Some research suggests that it does. The immune system is a complex network of cells that use particular molecules to communicate and to fight pathogens. The cells of the immune system are regulated through a system of chemical messengers, which allow the cells to communicate with each other and with the body (and vice versa). The immune system health and the gut microbiome are closely interconnected; they have to be so that the immune system doesn’t eradicate the ‘alien’ microbes in the gut.

When the gut microbiome is healthy, the immune system and the microflora interact positively. The immune system destroys unwanted microbes while supporting the growth of positive bacteria. The microbiome, in turn, supports the immune system. It sends out chemical messengers that help the immune system to respond more effectively to pathogens while ignoring beneficial microbes and the body’s cells. This back-and-forth between the gut microbiome and the immune system helps keep both the bacteria colonies and the human host in good health. The system helps to protect the host against getting ill due to infections and also helps regulate the inflammatory response.

When things go wrong, the positive symbiosis between the body and the microbiome is disrupted. If the microbiome is depopulated (for example, by antibiotics), it can take time to rebuild, and the immune system can be weakened for a while. If a less beneficial microbe begins to overgrow in the gut, it can prevent those healthy interactions between the immune system and the gut biome. This disruption can make the body less able to fight off pathogens that cause disease. The immune system in your gut is less able to prevent infections from progressing; infections in the rest of the body may become harder to fight, too. Paradoxically, the immune system can also become more prone to attacking the body’s cells, causing autoimmune disorders. The precise interaction between gut flora and immunity is still not well-explored, but the connection between the gut and immune system is undeniable. If you’re suffering from issues with your gut and digestive system, or find that you’ve developed symptoms elsewhere in your body, it may be worth considering gut health as a possible cause. If you’re wondering how to improve gut health, you could try changing your food choices. A better diet, with a healthy balance of nutritious foods, plenty of fresh vegetables, and an emphasis on fiber, can assist beneficial bacteria in re-establishing thriving colonies. You might also speak to your doctor about trying probiotic foods and supplements. Probiotics introduce beneficial bacteria into your GI tract, where they can form colonies and help restore a healthy microbiome. Probiotics aren’t right for everyone, though, which is why you seek medical advice first.

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