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How Your Gut Health Is Linked to Your Immune System

How your gut health is linked to your immune system

Gut health is a hot topic these days, with an increasing number of researchers investigating how it can influence our health, including our immune systems. So you’ve probably already read or heard about the gut microbiota. But what is it exactly, how does it work with the immune system and are there ways of making it more effective?

The gut microbiota is the name for the community of micro-organisms (or microbes) that lives in the human gastrointestinal tract. There are approximately 100 trillion of these micro-organisms – which far outnumber the cells in a human body – including bacteria, viruses, fungi and parasites (i).

There are a few alternative terms for gut microbiota: gut flora or microflora, for instance, plus intestinal flora or gut bacteria. You may also have heard of the microbiome, though this refers to the collective genomes – complete sets of DNA including genes – of the micro-organisms in the gut.

Of these 100 trillion micro-organisms, most are bacteria. In fact, there are about 1,000 different species of bacteria in the microbiota, represented by around 5,000 different bacterial strains (ii).

So it’s probably no surprise that everybody’s microbiota is unique, with factors like your age, genes, diet, environment, health problems, exposure to stress and any medications you may be taking also affecting its composition. The microbiota has several important jobs, including metabolising nutrients from food and some medicines. It produces vitamin K too, which is important for blood clotting.

But that’s not all. It’s thought that the microbiota has many other roles to play, and scientists are discovering more and more about its importance for human health, including how other organs are influenced by the gut environment and how the microbiota may even help prevent and treat some diseases.

Indeed we’re just starting to discover how having a healthy or unhealthy gut can affect our wellbeing, including how the microbiota regulates human body homeostasis – that is, the state of stability, balance or equilibrium within the body that’s essential for life.

Does Gut Health Affect Your Immune System?

With up to 80 per cent of the body’s immune cells found in the gut (iii), scientists believe the human immune system has evolved alongside the microbiota to protect against disease-causing germs (pathogens), and that each supports and co-operates with the other (iv).

This co-operation – or ‘conversation’ – between the immune system and the microbiota is thought to start the moment we’re born, when our bodies are first introduced to microbes. Then as we grow, our microbiota affects how our immune systems develop, while at the same time our immune systems affect the composition of our microbiota (v).

This process continues for the rest of our lives, with the immune system helping to maintain a stable microbiota and the growth of beneficial micro-organisms and the microbiota producing molecules to support the development of immune cells and improving how the immune system responds to invading pathogens (vi).

In other words, the relationship between the immune system and microbiota helps protect us against things like bacterial and viral infections. But it also helps the gut to tolerate harmless micro-organisms and even encourages our immune system to not attack healthy tissues in the body (when the immune system behaves this way it’s known as autoimmunity, with rheumatoid arthritis and psoriasis two examples of autoimmune disease).

The Intestinal Barrier

The gastrointestinal tract is lined with a layer of tightly packed cells called epithelial cells that produce mucus. So if a pathogen has managed to get past the immune system’s first line of defence – including the skin, mucous membranes and stomach acids – and as far as the gut, it must then penetrate this sticky lining before it can go any further and cause an infection.

The epithelial cells along with some immune cells also produce a chemical barrier by releasing antibodies, inflammatory molecules called cytokines and other antimicrobial substances, all of which try to stop the progress of invading pathogens.

Certain immune cells also help to maintain the intestinal barrier, including M cells (microfold cells), dendritic cells, and B and T cells that live in the intestinal wall. You can find out more about the cells and organs of the immune system by reading Understanding how the immune system works.

Diet and Gut Bacteria

Your gut microbiota helps your body digest much of the food you eat, and at the same time gets most of the nutrients it needs itself from your diet. In fact, scientists believe diet has a major impact on the composition of your gut microbiota, and consequently your immune system (vii).

Many nutrition experts suggest having a lot of variety in your diet is a good way of keeping your gastrointestinal microbiota healthy, and that a lack of microbiota diversity could lead to health problems and disease (viii). So one way to support your gut flora may be to eat at least five portions of different fruits and vegetables every day (the more portions and the more variety the better).

Fruits and vegetables are ideal sources of nutrients for your microbiota because they’re high in fibre. Your body may not be able to digest fibre, but many of the organisms in your microbiota love it, feeding on it and breaking it down. Beans, legumes and whole grains are gut-friendly foods, as they too contain high amounts of fibre.

Foods that help promote the growth of beneficial bacteria in your microbiota are also often called prebiotic foods. These contain different dietary fibres such as inulin, fructo-oligosaccharides (FOS) and beta glucans:

  • Inulin is found in foods such as Jerusalem artichokes, asparagus, leeks, onions and bananas, and is classed as a fructan compound. Indeed scientists believe there’s evidence that fructans have immunomodulatory properties (ix).

  • Also a fructan compound, FOS is made up of short fructose chains and has a naturally subtle sweet taste. There are several theories as to how FOS may affect the immune cells found in the gut – for instance they could activate certain immune cells and help improve the quality of the immune barrier, as well as help reduce intestinal inflammation. Studies meanwhile suggest FOS and other prebiotics may help boost immunity against viral infections such as the flu (x). Researchers elsewhere have found a nutritional supplement containing FOS may increase the number of immune system antibodies in people aged 65 and older (xi). There’s also evidence that FOS may help relieve the symptoms of diarrhoea in children (xii).

  • Beta glucans are compounds found in baker’s yeast, grains such as oats, barley rye and wheat, as well as some mushrooms (eg shiitake) and seaweed. Increasingly thought to be important for immune health, beta glucans have been studied since the 1960. Researchers have found they may have various effects on the human immune system (xiii), and that they may trigger and enhance the function of some immune cells (xiv).

Beta glucans may even help reduce the symptoms of common cold infections, with experts investigating firefighters finding those taking beta glucans had 23 per cent fewer colds than others taking a placebo (xv).

Fermented Foods

You may also be able to top up your microbiota with foods that contain beneficial living micro-organisms or live bacteria (these are often called probiotics, or ‘good’ or ‘friendly’ bacteria).

Some types of live bacteria have been found to help boost the immune system and reduce the risk of viral infections, with studies suggesting they may help prevent and relieve symptoms of colds and other infections (xvi). Another study suggests taking certain types of live bacteria may shorten the length of a cold by almost two days as well as reduce the severity of symptoms (xvii).

These beneficial live bacteria come in many strains, and have names such as Lactobacillus acidophilus, Lactobacillus paracasei, Bifidobacterium longum and Streptococcus thermophilus. One particularly good source of live bacteria is fermented foods. That’s because during the process of fermentation, bacteria and yeasts convert carbohydrates such as starch and sugar into alcohol or acids. This gives fermented foods their distinctive, tangy taste, while promoting the growth of beneficial bacteria.

Examples of fermented foods include:

  • Live natural yoghurt

  • Sauerkraut

  • Tempeh

  • Kefir

  • Kombucha

  • Kimchi

  • Pickles

  • Apple cider vinegar

Supplements containing live bacteria are also available, such as acidophilus capsules (look for a high-strength supplement with billions rather than millions of live bacteria per dose).

Meanwhile being physically active may help boost your gut microbiota too. In one study, for instance, exercise – especially when combined with a protein-rich diet – was found to boost the amount and number of different types of gut bacteria (x).

Find out more about how exercise can help support your immune system by reading How can you strengthen your immune system?


Natural Support For Immunity

Besides keeping your gut microbiota healthy and balanced there are other things you can do to support your immune system, such as using nutritional and herbal supplements. Some that may be helpful include:


A popular medicinal herb, echinacea is used to relieve the symptoms of the common cold and influenza-type infections, based on traditional use only. There is also some evidence that various forms and species of echinacea may reduce cold symptoms and help you get over a cold faster (xix). One study also suggests taking echinacea as a long-term preventative may reduce the number of colds you catch (xx).

Vitamin D

Best known for maintaining bone health by helping the body absorb calcium, vitamin D is also thought to play a part in regulating your immunity, with deficiency associated with autoimmune issues as well as an increased susceptibility to infection (xxi).

Vitamin D deficiency is thought to be common in some countries including the UK, which is why the Scientific Advisory Committee on Nutrition advises that adults and children over the age of four should consider taking a daily supplement containing 10mcg of vitamin D throughout the year (xxii).

The recommended form of vitamin D is vitamin D3 or cholecalciferol, as it’s the natural form of vitamin D that the body makes when it’s exposed to sunlight. Vitamin D3 supplements are available in tablet form, and now you can get them in veggie-friendly drops too.

However, most vitamin D3 supplements are made from the fat of lamb’s wool, which means they’re unsuitable for vegans. The good news is that vegan vitamin D3 supplements sourced from lichen are now more widely available.


Elderberries – which grow on the Sambucus tree – have a long traditional use for the relief of colds and flu. One study investigating the effect of an elderberry extract found it reduced flu symptoms by three to four days, and that it might also be beneficial for the immune system by increasing the production of immune cells (xxiii).

Discover more about how your diet and nutritional supplements could support your immune system in Can antioxidants support the immune system? There’s also lots more to find out about a range of health issues in our pharmacy health library.


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Disclaimer: The information presented by Nature's Best is for informational purposes only. It is based on scientific studies (human, animal, or in vitro), clinical experience, or traditional usage as cited in each article. The results reported may not necessarily occur in all individuals. Self-treatment is not recommended for life-threatening conditions that require medical treatment under a doctor's care. For many of the conditions discussed, treatment with prescription or over the counter medication is also available. Consult your doctor, practitioner, and/or pharmacist for any health problem and before using any supplements or before making any changes in prescribed medications.

Our Author - Christine Morgan


Christine Morgan has been a freelance health and wellbeing journalist for almost 20 years, having written for numerous publications including the Daily Mirror, S Magazine, Top Sante, Healthy, Woman & Home, Zest, Allergy, Healthy Times and Pregnancy & Birth; she has also edited several titles such as Women’ Health, Shine’s Real Health & Beauty and All About Health.

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