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The User-Friendly (Paleo) Guide to Your Immune System

A guide to your immune system

Most of us rarely appreciate our immune system until something goes wrong. We mostly notice it when it breaks down: when we catch a cold, or during the seasonal scramble for Vitamin C supplements in October and November. But if the immune system only existed for the first few weeks of chilly weather every year, we’d all be in serious trouble – every day, it’s busy keeping us healthy and functional, and protecting our bodies against the constant pressure of hostile organisms like viruses and bacteria.

In such a sophisticated system, there’s a lot to go wrong, from major autoimmune disorders like Type 1 Diabetes to minor irritations like a winter cold. Inevitably, some pathogen will make it past your body’s defenses long enough to get you sick. But there’s a lot you can do to keep your immune system functioning as well as possible, and most of it has nothing to do with Emergen-C and Air Borne. A Paleo diet reduces the strain that modern toxins place on your immune system, letting it focus on staving off the flu going around the office instead of worrying about gluten in your bloodstream. Combining that diet with adequate sleep and rest leaves your body fully charged and ready to tackle any combination of antigens – no pharmaceuticals required.

Mom, Dad, This is my new Helper T Cell: Meet Your Immune System

Every day, your body is exposed to an uncountable number of antigens, foreign invaders that have the potential to make you sick. Viruses, bacteria, parasites, and other disease-causing organisms are all antigens. Unless you live in a completely sterile environment (and unless you’re a transplant patient in a hospital, you don’t), your body has to fight off antigens from everything you touch, eat, drink, or breathe. For example, say you use the bathroom in a restaurant. When you open the door to leave, you touch the door handle. If the last person in that bathroom had strep throat, those streptococcus bacteria just became your problem.

Fortunately, you have a highly sophisticated mechanism for fighting them off, otherwise none of us would ever be healthy. Your front line of defense is the innate (or nonspecific) immune system, an all-purpose reaction to anything that comes at you. This includes physical barriers to infections like the skin and mucus membranes, and also the lining of the intestinal tract. Before the bacteria on that door handle can make you sick, they have to get inside your body, and the innate immune system makes this very difficult. But say you leave the bathroom, and go back to your dinner, and pick up an apple to eat it. This gives the strep bacteria a perfect avenue into your system.

Innate immunity will continue to protect you against the bacteria with nonspecific defense mechanisms like inflammation. Inflammation is an all-purpose immune response: it creates an additional physical barrier, and the chemicals associated with it attract a type of cells called phagocytes, which essentially neutralize foreign invaders by eating them. Inflammation gets a lot bad press in the Paleo community, but this kind of inflammation isn’t actually harmful: it’s only bad if it becomes a chronic problem (something that continues into the long term, rather than arising only in response to a short-term threat).

Once the bacteria are inside your body, they also have to face down an even more formidable enemy: the adaptive immune system. Where the innate immune response is a collection of one-size-fits-all reactions, the adaptive immune system has a custom response for each type of antigen. The innate immune system is largely determined by genetics (you inherit it from your parents), while the adaptive immune system learns from its experiences with different pathogens.
It takes longer to respond, but it’s often more effective.

The main actors of the adaptive immune system are a type of white blood cells called lymphocytes. Lymphocytes are formed in the bone marrow, and roughly divided into two major types: B lymphocytes, or B cells, and T lymphocytes, or T cells. Lymphocytes can travel all over the body, but they’re concentrated in areas called lymph nodes. If you’ve ever noticed the sides of your neck swelling up when you’re sick (or if a doctor has ever checked you for “swollen glands”), you’ve found one set of lymph nodes.

B lymphocytes have a wide variety of different types: each type responds to a specific antigen by making a specific kind of antibody. Antibodies are molecules that bind to foreign invaders: they don’t destroy the antigens, but they start the process of getting rid of them. If you’ve ever had strep throat before, you’ll have B cells in your body that remember it: they’ll immediately recognize the invading streptococcus bacteria and produce antibodies to them.

Antibodies are nice, but to prevent or recover from a disease, you need to kill the bacteria, not just recognize them. This is where the T cells come in. There are two types of T cells. Helper T cells are the immune system’s secretaries. They communicate with B cells, other T cells, and phagocytes to coordinate the immune response to a particular antigen. As their name implies, killer T cells aggressively attack antigens and destroy them.

This is a very broad and simplified outline of immune function (for example, there are actually several types of killer T cells), but serves well enough for most people who just want to optimize their diet, rather than conducting cutting-edge scientific research.

The Modern Diet, Leaky Gut, and Autoimmunity

As described above, the immune system has two major tasks: it has to recognize antigens, and then destroy them. Both tasks are equally important. If it can’t destroy antigens, the immune system is like a cannon without a bullet, but if it can’t recognize them properly, it’s like a cannon that someone is just shooting randomly into the air, hoping to hit the enemy – or worse, shooting at his allies because he’s mistaken them for enemies. Neither would be very effective as a weapon.

Unfortunately, the standard Western diet includes many foods that can make these two basic jobs much harder. Gut irritants like grains (especially gluten grains) and legumes are particularly harmful. These foods contain harmful chemical compounds called lectins. For example, Wheat Germ Agglutinin is a lectin found in wheat. Lectins found in several members of the nightshade family (such as peppers) also appear to be problematic for some people. In patients with Celiac disease (although not necessarily in the general population), another wheat protein called gluten also does the same kind of damage. All of these types of food toxins harm the immune system by causing the bad kind of chronic inflammation: they produce long-term irritation in the gut. This in turn leads to a larger problem known technically as “increased intestinal permeability” and informally as “leaky gut.”

“Leaky gut” is basically the failure of the intestinal wall to protect your bloodstream from toxins in the digestive system. The lining of the gut is one of the key players in the innate immune system. Just like the skin, the lining of the gut is a kind of barrier between your body and the outside world – when it’s working properly, it allows nutrients into your system, but keeps out toxins and pathogens that might be harmful. The cells of the gut wall are usually packed tightly together, preventing anything harmful from passing into your bloodstream, but when the gut becomes inflamed, the tight junctions between these cells loosen, and the intestinal wall becomes a less effective barrier against a variety of molecules and compounds that don’t belong in your blood.

When the intestinal wall is permeable like this, it allows certain types of proteins to pass through into the blood. The rest of your immune system recognizes that these proteins don’t belong there and attacks them. This would be bad enough on its own, because it puts a completely unnecessary stress on the immune system: when your body is busy fighting off foreign proteins in your bloodstream, it doesn’t have as much energy to tackle other pathogens you might encounter.

An even worse problem with leaky gut is the autoimmune response that often follows. The adaptive immune system responds to specific pathogens by recognizing their individual chemical signatures, but the proteins that can leak through the intestinal wall appear very similar to other cells that are natural and harmless parts of your own body. The similarity can essentially trick your immune system into attacking those cells too, a problem called autoimmunity. Leaky gut is a recognized contributing factor to all kinds of autoimmune diseases, including Type 1 Diabetes, Crohn’s Disease, and Rheumatoid Arthritis.

Gut Flora and the Immune System

Gut flora and healthAs well as including many inflammatory foods that contribute to leaky gut, the modern diet also contributes to autoimmune reactions and other immune problems in another way: it causes gut dysbiosis, or a disruption of the helpful gut flora that live in our intestines.

Gut flora are clearly linked to immune function and the prevention of leaky gut. Healthy gut flora support a functional intestinal barrier – they not only crowd out undesirable bacteria, but even actively help the gut destroy them. These friendly bacteria also help maintain the tight connections between the cells in the gut wall, shoring up the physical barrier to infection. On the other hand, disruption of the gut flora (especially bacterial overgrowth in the small intestine, abbreviated as SIBO) is linked to increased permeability. An overgrowth of bacteria in the small intestine actually causes the release of zonulin, the same chemical that regulates intestinal permeability in people with Celiac Disease who eat gluten. In other words, SIBO can provoke a Celiac-like leaky gut response even in people who don’t have Celiac disease or who aren’t eating any gluten.

As well as autoimmunity and leaky gut, some scientists have hypothesized that gut flora are also important in the development of allergic responses. They aren’t a disease, but allergies are a sign that the immune system isn’t properly differentiating between harmful pathogens and harmless environmental stimuli. Where an autoimmune response is an attack on a harmless part of your own body, an allergy is an attack on a harmless part of the outside world, like dust or pollen. One theory proposes that the modern lifestyle (extensive antibiotic use, C-sections that prevent mothers from passing on gut flora to their babies during childbirth, and a lack of traditional fermented foods) prevents the gut flora from developing normally, which in turn prevents the immune system from maturing properly. This has serious consequences for immune function, including a hypersensitivity to allergic triggers.

Scientists are still debating the exact mechanisms of gut-flora mediated immune function, but these bacteria are clearly involved in a healthy immune system somehow, and the modern diet and lifestyle doesn’t do them any favors. The antibiotics in our environment (including conventionally raised meat, antibiotic soaps and cleaning products, and other environmental pollutants as well as pills prescribed at the doctor’s office), the abandonment of traditionally fermented foods, and the damaging effects of a high-sugar diet all contribute to gut flora dysfunction that can contribute to the development of all kinds of immune problems.

Paleo and Immunity

While a modern diet contributes to immune problems, a Paleo diet helps to prevent and heal them – even the conditions less commonly recognized as problems with the immune system, such as eczema or psoriasis. A nourishing Paleo diet can also generally strengthen the immune system to reduce the number of colds, flus, and other antigenic annoyances you have to put up with.

For one thing, a Paleo diet that eliminates gut irritants like lectins prevents these foods from causing intestinal inflammation in the first place. Some people find it helpful to go even further, and embark on a Paleo autoimmune protocol. This is a slightly stricter version of Paleo that eliminates eggs, nightshades, and other foods that may be fine for most people, but gut irritants for someone already suffering from leaky gut-related autoimmune problems. Some people can eventually reintroduce some or all of foods after an initial elimination diet, but it can be helpful to cut them out at first.

As well as excluding gut irritants, all variations of Paleo also include several gut-healing foods that contribute to a healthy population of intestinal bacteria. Traditionally fermented foods like sauerkraut, kimchi, and kefir can help repopulate the gut with helpful bacteria, reducing the damage of antibiotics in the environment and helping arm the intestinal wall against any pathogens that come its way. Taking a probiotic supplement can also help: for example, in clinical studies, treatment with probiotics has helped patients suffering from allergies and Crohn’s Disease. A diet low in carbohydrates will also help eliminate SIBO or other bacterial overgrowth problems that contribute to gut dysbiosis and crowd out the helpful bacteria.

This doesn’t necessarily mean, however, that a zero-carb diet is optimal for immunity in people without SIBO or other gut flora problems. A ketogenic diet does starve unfriendly bacteria, but other types of pathogens actually prefer ketones to glucose. The immune system also needs glucose to fight these invaders, so a long-term low-carb diet can reduce the body’s ability to respond to them. Additionally, glucose is important for maintaining the mucous that lines the gut wall, one of the physical barriers to infection through the gut.

At first, this seems frustrating: which one should you pick? On the one hand, ketosis can help treat bacterial overgrowth and increases immunity to some pathogens; on the other hand, carbohydrate intake can promote the growth of beneficial bacteria and increases immunity to other pathogens. Fortunately, many people can actually get the benefits of both types of diet, by cycling their carbohydrate intake. Practicing intermittent fasting can give you many benefits of ketosis without requiring you to cut carbohydrates completely out of your diet. A moderate amount of safe starches when you aren’t fasting will satisfy your body’s need for glucose, giving you most perks of both a low-carbohydrate and a moderate-carbohydrate diet.

Of course, the nutrient content of your diet is also very important in maintaining a functional immune system. It’s not common to have such a severe deficiency in one particular micronutrient that it has a noticeable effect on immune function (although this does sometimes occur in developing countries); instead, most people suffer from multiple less severe deficiencies, which all interact with each other to impair proper immune function. This means that it’s not particularly useful to take enormous supplemental doses of Vitamin C or Zinc (two commonly touted “cold remedies”); most people would do better to eat a basically sound diet and shore up their levels of all important micronutrients, rather than trying to “hack” their immune systems by cherry-picking one or two to overdose in.

While you’re making sure to eat a diet rich in micronutrients, also try getting some more sun, or consider a Vitamin D supplement. Vitamin D is essential for a healthy immune system: it helps “arm” killer T-cells to destroy pathogens, and deficiency can even contribute to autoimmune disorders. It’s also the one micronutrient you probably won’t get enough of just from food, even if your diet is perfect. Although cold-water fatty fish contain some Vitamin D, by far the best source is sun exposure. Since most people spend the vast majority of their day indoors (especially in the wintertime), they don’t get nearly enough. A high-quality supplement or a consistent effort to spend more time in the sunshine will make sure you don’t become deficient in this vital micronutrient.

A high intake of healthy fats is another immune-boosting benefit of a Paleo diet. Getting plenty of fat – especially medium chain triglycerides, found in coconut oil – raises HDL, the beneficial kind of cholesterol that improves immune function and increases resistance to all kinds of infections and pathogens.

As with many health conditions, non-dietary factors can also be the elephant in the room. Sleep deprivation and chronic stress are inflammatory; even the strictest autoimmune protocol won’t help you if you’re skating by on 5 hours of sleep a night and 3 shots of espresso every morning. Getting adequate exercise (but not overtraining) and enough sleep every night to feel rested and awake in the morning can do wonders for your immune system. Medication can also be a culprit: although their name suggests the opposite, NSAIDs (Non-Steroidal Anti-Inflammatory Drugs) are actually recognized contributing factors to a leaky gut. Cutting down on your intake of painkillers in general is always a good idea, but if you do need one, try a non-NSAID option like Tylenol, which is easier on your digestive system.


The immune system is an incredibly complex network of cells, glands, and organs that has to keep us safe from an almost infinite number of pathogens every day. A high-sugar modern diet based on gut irritating foods like grains and legumes damages the intestinal lining and disturbs the natural balance of gut flora – both of these problems can lead to immune dysfunction. By eliminating these harmful foods and including plenty of nutrients and fats, a Paleo diet helps the immune system stay in peak condition to face down whatever comes its way.

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Hi I’m Ashley, I’m an ADAPT Certified Functional Health Coach

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