Poor gut health has been linked to poor immune function. In this article, we investigate the science behind this notion.
Let’s get started.
Did you know your body contains more microbial cells than human cells?
Yep. Your own body cells are outnumbered around 1:3 by micro-organisms.
The vast majority of these microbes live on the surface of your intestines, where they are actively involved in digestive and immune functions.
Between 30 and 40 different species of bacteria make up the majority of the microbiota. (“Microbiota” is the collective term for all the microbes in your intestines.)
These species are being studied intently by the scientific community to understand exactly how they influence your health.
Studies have highlighted the essential nature of the microbiota in the human digestive system, showing that they are intricately linked to nutritional status, inflammation levels, immune function, and even mood and energy levels.
Let’s take a look at 5 ways poor gut health and a disturbed microbiota can weaken your immune health.
Learn More: The Best Microbiome Testing Companies: Gut Testing Made Easy
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How Poor Gut Health Hurts Your Immune System
A Leaky Gut Leads Weakens Immune Health
Leaky gut occurs when your intestinal wall loses its integrity and the watertight joins between cells begin to loosen and form gaps. It’s like a patchwork blanket with the stitching coming loose. The gut wall has a very important function in making a barrier between the contents of your gut and your bloodstream. A healthy gut plans and orchestrates exactly which nutrients and molecules cross the barrier.
If you have poor gut health then your body can’t control what’s passing through into your bloodstream, so foreign particles cross the barrier at random. Your immune system recognizes that these substances shouldn’t be there and tries to neutralize them by responding as if you have an infection. This response doesn’t shut down as long as you have leaky gut; your immune system continues to react as if your body is threatened. Eventually, this leads to inflammatory and autoimmune diseases such as:
- Eczema
- Allergies
- Asthma
- Inflammatory bowel disease
Your Microbiota Is Part Of Your Immune System

When your microbiota is healthy and balanced, your normal beneficial bacteria take up all the space, nutrients and oxygen. There’s simply no room for disease-causing bacteria to move in. It’s likely they’re sometimes present in your gut but they starve before they have a chance to establish themselves. Your population of good bacteria also secrete unique chemicals that stop bad bacteria from growing. This prevents you from getting gastrointestinal infections.
Gut bacteria are also able to trigger your immune system to respond with more or less intensity. So, they can help to increase your immune response when you really need to be protecting yourself against a disease-causing agent. And they can also help to reduce your immune response when it’s unnecessary. Your immune system doesn’t always know when to respond and when not to, but it’s really important that it gets it right. Gut bacteria can help categorize threats and give your immune system the right instructions for how to respond. Without a healthy gut biota, you could be susceptible to the following illnesses associated with immune dysfunction:
- Fibromyalgia
- Chronic fatigue syndrome
- Thyroid disease
- Rheumatoid arthritis
Your Gut-Brain Connection Affects Immune Health
Your gut-brain connection is the way your gut influences the function of your brain. Understanding the connection is a new science and there’s still a lot to learn, but researchers have figured out that your microbiota is constantly sending complex signals to your brain by releasing neuroactive chemicals. These chemical messages have a powerful impact on your hormone balance, stress response and immunity.
A healthy gut sends signals to your brain encouraging resistance and resilience. Your body gets the message to make more immune cells when its being threatened by infection and to keep inflammation down even during stress.
When your gut health is poor, the chemical messages change and your gut-brain signals no longer contain instructions that help keep you healthy. Nervous system conditions that are associated with imbalanced gut bacteria and immune dysfunction include Alzheimer’s disease, multiple sclerosis, depression and autism.
Systemic Toxicity Reduces Immune Function
One of the most important functions of your gut is detoxification. All of the waste products from digestion of your food need to be removed from your body to keep you healthy. Other waste comes from the reactions that are going on inside your cells as they maintain themselves. A healthy gut can remove waste at a rate that’s fast enough to keep your blood and organs healthy and vital.
If your gut health is poor, then your detoxification pathways are congested and weakened. This means you won’t be able to remove digestive and cellular debris at the necessary rate and these damaging substances will build up in your system. This leads to inflammation, which weakens immune function, making you susceptible to diseases of toxicity. Common conditions linked to toxicity, inflammation and weak immunity include:
- Psoriasis
- Cancer
- Liver Disease
- Diverticulosis
Poor Nutritional Status Weakens Immunity

The major function of your gut is digestion. It takes the food you eat and breaks it down into its smallest parts, then carries it across your gut wall and into your bloodstream where your liver filters and sorts it. The process is complex and requires a vast number of different enzymes, acids, and cofactors to work efficiently.
Poor gut health means reduced amounts of some of these substances, which means you can’t digest your food properly. This can lead to a deficiency of one or more nutrients. Because your immune system needs good amounts of nutrients to function well, deficiencies can really impact your immune function. Illnesses associated with a deficient immune system include:
- Increased colds and flus
- Respiratory infections
- Skin infections
- Coughs and sinus congestion that don’t clear up
Take Home Message
Digestion is the seat of health, according to traditional western naturopathic medicine. What this means is that if digestion is functioning well, your body will be healthy.
Digestion is the foundation on which you build your immune system. And your immune system is at the center of your well-being. If you suffer poor gut health, then your immune cannot function normally and your chance of becoming sick increases greatly.
A good natural medicine practitioner will always treat the gut and digestion. They will know that even a condition that seems unrelated to the gut, such as Alzheimer’s disease, has a connection to intestinal health and the microbiota that dwells there.
The great news is that this concept is gradually being confirmed by scientific studies and becoming accepted as the new model for understanding health.
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