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Understanding How the Immune System Works

Understanding How the Immune System Works

Your immune system is an intricate network of cells, tissues and organs that has a very important job – protecting you against attacks by disease-causing substances such as bacteria, viruses, parasites (including fungi) and other micro-organisms.

If one of these substances – called microbes (or germs) – tries to invade your body, your immune system first tries to keep them out, and if that doesn’t work it then tries to destroy them.

Not all microbes are harmful - according to the UK’s Microbiology Society, fewer than one per cent of bacteria can invade the human body and make you ill (i). But those that are capable of causing infections – the most common cause of human disease – are called pathogens. Examples of common pathogens include rhinoviruses, which cause the common cold, coronaviruses (including the SARS-CoV-2 virus that causes the Covid-19 infection), the varicella zoster virus (chickenpox), Mycobacterium tuberculosis (TB or tuberculosis), Trichophyton rubrum (a fungus that causes ringworm) and Trichophyton mentagrophytes (athlete’s foot).

The organs of the immune system are found throughout the body and include:

  • Skin and mucous membranes

  • Lymph nodes and lymphatic vessels

  • Spleen

  • Thymus

  • Bone marrow

  • Tonsils and adenoids

Meanwhile some of the cells that are part of the immune system include:

  • Lymphocytes (B cells, T cells and natural killer (NK) cells)

  • Phagocytes (including macrophages and granulocytes)

  • Cytokines


How the immune system works

Luckily for us, pathogens contain antigens. These are molecules found on the surfaces of pathogens that tell your immune system it’s under attack. They are also important components of the pathogen that help it infect your cells – for instance, influenza antigens are protein molecules that help the virus enter a cell.

When the immune system is activated by the presence of a potential threat in the form of an antigen, what happens is called an immune response. And the first line of that response is your skin.

For a pathogen to enter the body, it must get past your skin. Usually the only way it can move past this barrier is to penetrate the skin through cuts or small abrasions. A pathogen can also get into the body through entry points such as the nose, which is lined with cells collectively called a mucous membrane. If the immune system senses a threat in the nose, these membranes secrete mucus, a sticky substance designed to trap pathogens and kill them. It can also trigger sneezes and coughs that help to physically force foreign invaders out of your respiratory system.

Meanwhile if you eat food that’s infected with pathogens (bacteria, for instance) the strong acid your stomach produces to help with digestion can often kill them before they can progress any further.

If a pathogen breaches all of these front-line defences, the next obstacle it has to overcome is the layer of mucus that covers the tightly packed cells (called epithelial cells) that line your digestive, respiratory and urogenital tracts. To reach and infect the underlying cells, a pathogen has to get through these mucosal surfaces, which can also secrete a type of antibody called IgA. If it’s successful, the pathogen then has to face an army of immune system cells before it can reach its target, including macrophages, B cells, T cells, phagocytes and NK cells.

Methods of attack

Your immune system can recognise and remember millions of different pathogens and their corresponding antigens, the most common of which in terms of human disease are bacteria, viruses and parasites. All of these work differently to cause an infection, but thankfully the immune system knows how to deal with each one of them.

Bacteria, for instance, are largely tackled by antibodies. These attach themselves to bacteria and send signals to other immune cells – including phagocytes – to destroy them. The phagocytes also signal some T cells, which also attack the bacteria.

Most bacteria live in the spaces between cells, but viruses – and a few types of bacteria and parasites – must get inside cells or they die. Antibodies can attach to viruses before they have a chance to enter any cells, which helps the immune system to destroy them before they can do any harm. But if a virus does infect a cell or number of cells, the cells can use protein molecules called major histocompatability complex (MHC) molecules to place fragments of the virus or other pathogens that have invaded them on their cell surfaces. These fragments are recognised by T cells, which then try to destroy the infected cells.

Parasites, meanwhile, can live either inside or outside cells. When one invades a cell, T cells are called into action to destroy it. But parasites that live outside cells trigger a bigger immune response, with antibodies attracting several types of granulocytes to the site. These immune cells – which include basophils and eosinophils – release toxic chemicals that can trigger an inflammatory response to help destroy the parasite. 

Immune system cells

There are several types of cells in the immune system that work together to fight infections and other illnesses. These cells identify, mark and destroy pathogens that either enter the body or develop inside the body. Some of the main immune cells include:


If you’ve been exposed to a disease-causing organism before, immune cells called lymphocytes (also called adaptive cells) make antibodies that fight the infection should you come into contact with it again. Lymphocytes – which are a type of white blood cell – also attack viruses and other pathogens. There are two main types of lymphocytes – T cells and B cells.

T cells

These are produced in your bone marrow but travel to an organ called the thymus, where they develop and mature. They attack pathogens directly, but they need help from other cells to recognise them. Once they have been activated, they expand and start to divide, then release chemicals that destroy the pathogen they’ve been alerted to. Some of these cells form a ‘memory’ of the pathogen, so if it invades your body again your body can respond quickly to it

Meanwhile, your immune system also includes regulatory T cells (Tregs), which monitor other T cells. When necessary these cells stop other T cells working, which can prevent your immune system being activated unnecessarily.

B cells

Your immune system’s B cells make chemicals called antibodies. Antibodies are special proteins that lock on to molecules called antigens, which are found on the surface of pathogens, and ‘flag’ them for death. Antibodies belong to a large family of chemicals called immunoglobulins that have various roles in the immune response (examples of immunoglobulins include IgA, IgD, IgE, IgG and IgM).

So when a B cell recognises an antigen, it binds to its surface. The B cell then changes into a plasma cell that makes antibodies that target that particular antigen. The antibodies also activate other immune defences, including encouraging other cells to destroy the pathogen.

Each B cell makes one specific type of antibody. Experts also believe B cells can recognise millions of different antigens, including those that have never entered the body before and even man-made antigens (ii).

Another type of lymphocyte is called a natural killer cell (or NK cell), which – like killer T cells – release chemicals to attack several types of foreign cells.


Also a type of white blood cell, phagocytes can kill viruses, bacteria and other harmful organisms as well as normal body cells that are no longer useful. Two examples of the various types of phagocytes include:


These start out as cells called monocytes but develop into what we know as macrophages, which means ‘big eater’ in Greek. They’re found in the bloodstream and in tissues and can eat and degrade bacteria. Not just that - but macrophages signal other immune cells when they find a problem. They also recycle dead cells – such as red blood cells – and clear away other cellular debris.

Monocytes can also develop into dendritic cells. These help both the B and T cells by ‘showing’ them antigens, allowing the B and T cells to attack the pathogens the antigens are attached to.


These are classed as immune cells called granulocytes (other examples include basophils – or mast cells – and eosinophils). They are found in your bone marrow and, like macrophages, circulate in the bloodstream, looking out for problems and ‘eating’ bacteria.


These are proteins, or chemical messengers, that allow components of the immune system to communicate with one another. Various types of cytokines found in the immune system include interleukins, interferons and growth factors. Some cells release cytokines at a site of injury or infection, which sends signals to other cells to help repair damage or fight off a pathogen. Others – such as interleukin 2 – send messages to the immune system to produce T cells.

Immune system organs and tissues

Your immune system also relies on a number of tissues and organs that work together to help immune cells protect the body against invading pathogens. The main organs and tissues of the immune system include:


Often described as the body’s largest organ, your skin is your immune system’s first line of defence against pathogens. Your skin provides a barrier defence against invaders and produces oils that can help kill them.

A second physical barrier that protects against infection is made up of mucous membranes, which are the soft, moist linings in parts of your body including your mouth, nose, gut and airways. Some of your mucous membranes produce mucus, a sticky substance that traps bacteria, viruses and parasites and contains cells and proteins that attack and destroy them.

Bone marrow

Found inside the bone, bone marrow is a soft substance that’s an important part of the immune system. It produces stem cells that develop into a variety of different cells, including immune system cells such as neutrophils, monocytes, dendritic cells and macrophages, as well as adaptive immune cells including B and T cells. It also produces red blood cells that transport oxygen around the body, and platelets that are necessary for blood clotting.


Your bloodstream transports immune cells that are constantly circulating and looking out for pathogens. Taking a sample from your bloodstream can also show if you have any problems with your immunity – it can, for instance, show if you have too many or too few white blood cells.

Lymphatic system

A network of vessels and tissues, the lymphatic system is an important component of your immune system. It contains a non-cellular fluid called lymph as well as hundreds of small glands called lymph nodes, where T cells ‘learn’ to recognise and destroy invading organisms. The lymph nodes also help to filter out viruses, bacteria and cancer cells so they can be destroyed by immune cells.


Your thymus is a small organ found at the front of your windpipe and is classed as a lymphatic organ. It provides a home for your T cells after they’ve been produced in your bone marrow, and ‘teaches’ them to tell the difference between normal body cells and potentially harmful foreign cells that invade the body.


A large mass of tissue, the spleen is found just under your rib cage on the left side of your body. It helps to filter your blood and processes information from the bloodstream, while providing storage for platelets and white blood cells. Some immune cells such as B cells multiply in the spleen. 

Immune system disorders

Some people develop or were born with an immune system disorder, which can affect the way their immune system works.

Primary immunodeficiency

This is the name for having a weak immune system from birth. These are rare, genetic disorders that can be diagnosed either in children or in adults. There are around 300 different PIDs, all of which affect how the immune system works (iv). Nobody knows exactly how many people have PID in the UK. More than 4,300 people are registered on the UK Primary Immune Deficiency Registry (iii), but many may go undiagnosed because they have a mild form of PID that allows them to lead a relatively normal life.

Acquired immune deficiency

You can develop immune deficiencies if, for instance, you take certain medicines (chemotherapy drugs, for instance), if you smoke, drink alcohol excessively or if you have poor nutrition. Some infections such as the flu can also weaken your immune system, but thankfully the effect is only temporary.

Overactive immune system

People who have an overactive immune system usually have allergies. These can include asthma, eczema and allergic rhinitis (either seasonal, caused by pollen, or perennial, which can be triggered by things like dust mites, pet dander or moulds).

Autoimmune disease

Autoimmune disease is when your immune system attacks normal, healthy tissues rather than pathogens or infected tissues. Nobody knows exactly what causes this to happen, but there may be many factors involved, such as your genes and your environment. Autoimmune diseases include type 1 diabetes, rheumatoid arthritis and lupus.

In type 1 diabetes, the immune system attacks cells in the pancreas that make insulin. In rheumatoid arthritis they attack the joints, causing swelling and joint deformities. Lupus, on the other hand, is when the immune system attacks several body tissues, including the lungs, kidneys and skin.

How to protect your immune system

If you have a weak immune system you may be susceptible to frequent infections and more severe infection symptoms, which can make your illness difficult to treat. Typical infections that can affect someone with a weak immune system include pneumonia, bronchitis, skin infections and meningitis.

Having a weak immune system can also make you more likely to experience other problems including blood disorders such as anaemia, digestive problems such as diarrhoea and loss of appetite, and inflammation of the internal organs.

If your immune system isn’t as strong as it should be, it’s essential to stay as healthy as possible and to try not to come into contact with bacteria, viruses and other organisms that cause infections. You can’t always avoid these things, however. But you can reduce your risk of being infected by them if you practise good hygiene.

Washing your hands is one of the best ways to protect yourself from being infected by a pathogen, including the virus that causes Covid-19. That’s because these germs are easily spread from one person to another when someone who’s infected touches a surface, and another person then touches the surface and transfers the pathogen to their eyes, nose or mouth.

To keep yourself safe – whether you have a weakened immune system or not – it’s a good idea to wash your hands or use hand sanitiser that contains at least 60% alcohol at the following times (iii):

  • Before, during and after preparing food

  • Before eating

  • Before and after looking after someone who has diarrhoea or vomiting

  • Before and after treating a cut or wound

  • After using the toilet

  • After changing a baby’s nappy

  • After blowing your nose, coughing or sneezing

  • After touching an animal, animal feed or animal waste

  • After handling pet food or pet treats

  • After touching rubbish or using a rubbish bin

If you have a weak immune system, it’s also a good idea to avoid people who have an infection such as a cold or flu as much as possible. If you can’t avoid them altogether, try not to have any close contact with them or share food or drinks with them until they’re feeling better.

Natural immune system support

Taking a nutritional supplement may be another weapon you can use in the fight against germs and infections. First, try a daily multivitamin and mineral supplement, as this may be helpful if you’re not getting all the essential nutrients you need from your diet (if you’re not eating as healthily as usual for any reason, for instance). Look for a supplement that contains good levels of selenium, zinc as well as all the main vitamins.

Other supplements that may be useful 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 (iv). One study also suggests taking echinacea as a long-term preventative may reduce the number of colds you catch (vii).

Vitamin C

An essential nutrient that’s needed for many processes in the human body, vitamin C is believed to contribute to immune defence. It supports various functions of both the innate and adaptive immune system, with deficiency leading to impaired immunity and a higher susceptibility to infections (viii). Studies suggest that vitamin C and zinc (see below) may make you more resistant to some infections such as the common cold, as well as shorten their duration (ix).

Your body cannot make vitamin C, so it has to come from food and from vitamin supplementation. Many fruits and vegetables contain vitamin C, including berries, peppers, tomatoes, citrus fruit, kiwi fruit, broccoli and potatoes.

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 innate and adaptive immunity, with deficiency associated with autoimmune issues as well as a greater susceptibility to infection (x).

However, 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 (xi).

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 called cytokines (xii).

Live bacteria

The millions of micro-organisms and bacteria that live in your digestive system are thought to play a key role in immune response, as well as your overall health and fitness. Indeed, experts believe around 80 per cent of immune tissue is found within the digestive tract (xiii).

Acidophilus and other types of live bacteria are thought to help boost the immune system and reduce the risk of viral infections, with some studies suggesting they may help prevent and relieve symptoms of colds and other infections (xiv). One study also 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 (xv).

Food sources of live bacteria include yoghurt, kefir, sauerkraut, miso and tempeh, but nutritional supplements that contain live bacteria are also popular.


An important mineral for human health, zinc is also considered essential for immunity. In fact, there’s strong evidence that zinc deficiency plays a major part in immune dysfunction in humans (xvii). One study of zinc deficiency in humans also suggests it may result in immune dysfunctions, mainly affecting T cells (xvii).

Foods rich in zinc include meat, shellfish, legumes, nuts, seeds, dairy foods, eggs and whole grains. However, many people may not be getting enough in their diet. If you’re thinking of trying a zinc supplement, look for the mineral in its citrate form, as this is believed to be absorbed by the body more easily than some other forms.

Beta glucans

Natural compounds called polysaccharides that are found in baker’s yeast, grains such as oats, barley, rye and wheat, as well as some mushrooms (shiitake, for instance) and seaweed, beta glucans (or β -glucans) are increasingly thought to be important for immune health.

While they may not be as well known as some other nutritional compounds, researchers have been interested in beta glucans since the 1960s. Several studies have shown that beta glucans have various effects on the human immune system, including protecting against infection and stimulating the immune system to respond to pathogens (xviii).

Researchers have found that, among their various actions, they trigger and enhance the function of immune cells including macrophages, neutrophils, monocytes, natural killer cells and dendritic cells (xix). A review of studies into beta glucans has also concluded that they appear to be effective at enhancing immune function and reducing susceptibility to infection and cancer (xx).

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

For more information and advice on a range of health issues, visit 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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