Certain components in grains can disrupt your digestion and inhibit nutrient absorption. Read on to understand how.

Grains contain a number of protective components that humans cannot fully digest, rendering them a problematic staple in our diets. In this article we look at the anatomy of a grain with a particular focus on the components of grains that present issues for human digestion. 

A grain is an organism

Like all other organisms they exists to reproduce. Grains have three main components that facilitate this: the bran, endosperm and germ act as a reproductive centre and a protective mechanism.

Grain biology 

14% Bran (outer shell)

The outside shell of an unprocessed grain, which is designed to protect it grain from being eaten. It contains a number of vitamins and minerals, which is why on face value grains appear nutritionally richer than they are. However, the bran also contains proteins (such as lectins) and anti-nutrients (such as phytic acid), which inhibit your ability to absorb minerals and vitamins. They can also be severely irritating to your digestive system (see below).

83% Endosperm (inside)

This makes up the bulk of the grain biology and is where the energy supply of the grain is located. It is mainly starch and some protein.

3% Germ (reproductive core)

Where the grain embryo is stored. For a grain to grow, the endosperm supplies energy to the germ.

The protective mechanisms of grains

These are the components of of grains that are problematic for human digestion. Everything in nature has its own defence mechanisms, whether small or large, to ensure the species continues to propagate. Grain biology is no different. Animals have the ability to run away, hide or deter predators in a variety of interesting ways. Plants are a little more complicated, but not much. Many fruits, such as berries for example, are able to reproduce because their seeds pass through the animals that eat them and are then fertilised. This is how blueberries propagate their seeds and eventually reproduce. Other plans such as poison ivy defend themselves and hence ensure reproduction in a more obvious way, they have mechanisms to stop them being eaten in the first place. This needs no explanation. 

Grains on the other hand are more complex. But do not be fooled, they do have the means to protect themselves, so there are a few components that stop you from being able to fully break them down. This allows elements of the grain to pass through your system fully intact, which can cause problems for your body. Let’s take a look at these elements in detail.


Lectins are contained in the outer layer (the bran) of the grain or sometimes in the germ. They are a variety of protein that is particularly nasty for the human digestive system.

Lectins are a glycoprotein – a complex protein that contains a simple carbohydrate combined with a simple protein. They are thought to be a way for the seeds of grains to remain complete, so they can pass through animals systems and then reproduce. This is important for the grains to be able to propagate their seeds, but humans do not want to be eating things that we cannot digest properly. Lectins such as wheat germ agglutinin (WGA) are found in the germ to protect the grain from insects and other potential predators. They can be problematic for the humans that eat them too.

Lectins are not properly broken down during our digestive process, so they enter the gut as large proteins. We lack the appropriate enzymes to fully break these proteins down, perhaps a sign that we shouldn’t be eating too many. When things enter our digestive system intact they can cause flatulence and bloating (lentils and beans anyone).

Because the walls of our gut a slightly permeable (to let in the good nutrition) the lectins that are not broken down can actually be transported, fully intact, through our digestive lining. When the lining of the digestive system is compromised, it is referred to as intestinal permeability or ‘leaky gut.

While it is important that some nutrients are absorbed through the digestive tract, we do NOT want things like lectins getting into our system because they trigger an immune response. Normally, proteins are broken down into short chain amino acids in our stomach by digestive enzymes before they are absorbed into our system.

Once past the protective layer of the digestive system and in the body lectins can be mistaken by our immune system as foreign bacteria or viruses. Our immune system can then create antibodies against these proteins. As your white blood cells launch an immune response to the ‘foreign’ invaders they release free radicals, which leads to inflammation in the body. Chronic inflammation leads to a whole host of other conditions such as autoimmune disease.

The degree to which lectins can breach the walls of your gut varies significantly between individuals. Obviously we can’t blame grains for all of our illnesses, but there are now thousands of stories of people fixing very serious health complications such as autoimmune disease, simply by removing grains and other lectin containing foods from their diets.

Lectins are also found in legumes, beans, some diary and nightshade vegetables. Nightshades include white potatoes, tomatoes, aubergine and red peppers; however, unless you are experiencing health complications the benefits you get from these vegetables outweighs any risks. Genetic modification of many of the foods we eat today has increased the number of lectins in our grains so cutting down is  a good move.


Also known as phytic acid is the main storage form of phosphorous in many plants and acts as a mineral-binding compound. Phytates bind to minerals like magnesium, iron zinc and copper and prevent your body from absorbing these essential nutrients. This means that you are not only missing out on the minerals from the grains, but they are also stopping you from absorbing minerals from the rest of your food.

Phytic acid also disrupts some of the enzymes used to digest our food, which prevents proper breakdown of proteins in the stomach. Trypsin, the enzyme required for digestion in the small intestine is also affected. While soaking or sprouting grains can be a good way to reduce the amount of phytic acid in them, it is better to limit your consumption and instead choose whole foods such as meat and vegetable where nutrition is not compromised.


Zonulin is a protein that alters the tight junctions of the intestine and increases permeability of the digestive tract (see diagram above). It is activated by Gladilin, which is a glycoprotein found in wheat. Increased intestinal permeability, or leaky gut, can result in a huge array of conditions – read more here. Due to the increased gut permeability that results from zonulin, it is gradually being associated with various auto-immune diseases such as type 1 diabetes.  These new discoveries actually challenge the traditional thinking that autoimmunity results from genetic makeup or environmental triggers. It highlights the critical importance intestinal barrier for protecting our health and the dangers that things like gluten pose.

Saponins and protease inhibitors

Saponins and protease inhibitors are found in some of the non-gluten containing grains such as rice, corn, quinoa, aramanth, buckwheat as well as legumes and some vegetables. Like lectins they are part of the plant’s defence mechanism, which also prevent your body from fully breaking the seeds down and contributing to leaky gut. Obviously you cannot avoid these entirely, but it is yet another reason why limiting your consumption of all grains is a good idea.


Gluten is a protein found in wheat, barely, rye and in trace amounts of many other grain products. Gluten makes up about 80% of modern day wheat products. Many of us lack the right enzymes to properly break down gluten and it is responsible for a host of problems far beyond just celiac disease. Gluten can be so problematic that it needs a dedicated explanation. You can read mine here.

Final words on grain biology

Contrary to what we have been taught whole grains are not a healthy food. Nature gave them minimal defence mechanisms, but those that they do possess are intended to prevent humans from breaking them down properly so that the grain has the chance to survive. The compounds discussed above such as lectins, phytates and saponins work to protect parts of the grain, but end up causing trouble for our digestion. Like grains, lectins, beans and nuts also contain many of these problematic compounds.

There are certain methods we can employ to reduce the number of these problematic compounds such as soaking foods before we consume them; however, my approach is to try and limit my consumption of grains, legumes and beans most of the time. I consume nuts occasionally because they provide other benefits.

If you feel well and full of energy then you don’t need to immediately cut out grains. However, it is worth being armed with a real understanding of exactly what you are putting in your body – particularly when it has been sold to you as a ‘healthy’ choice.

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