The following blog covers Assimilation, one area of the Functional Medicine Matrix which I talked about a little bit about in an earlier blog . I wanted to spend some more time exploring these areas or ‘nodes’ separately and in slightly more detail as each are extremely important. And so, in writing this post, I’ve gathered information from a number of sources to give an in-depth summary with more detail than in the previous blog. It’s by no means an exhaustive study on the subject of Assimilation but will provide a good jumping off-point for further discussion.

What is Assimilation?

Assimilation in this context refers to how our bodies take in and process what is provided through their environment. It’s all to do with how the body breaks down these components and uses them within our system, through the transferral of nutrients via enterocytes (cells which line the walls of the gut) into the bloodstream where they are used as energy.

Assimilation mainly takes place within the gut, which is part of the digestive system and can be up to 30 feet in length in adults. As digestion can take anything from 24-72 hours, with food travelling from one end of the digestive system to the other, a fundamental belief of Functional Medicine is that because everybody’s system works differently, a personalised diet is crucial to a happy, healthy gut. Understanding what goes on in our bodies during these hours, as well as what may be going wrong helps us work out imbalances and leads us to a diet that’s more suitable.

The Process of Digestion – and Where Things Can Go Wrong

The process of digestive begins earlier than you might think.

From the moment that you think about or smell food, digestive juices start to be produced. When we eat and when we chew, both the mechanical and chemical breakdown of the food ingested (particularly of carbohydrates) begins.

Eating Mindfully

Eating mindfully is an important first step to improving assimilation – after all, if we don’t think about eating, we don’t think about chewing and if we don’t think about chewing we’re already causing problems that our digestive system will need to deal with further down the line.

Stomach Acid & Enzymes

After swallowing, the food reaches the stomach where digestive juices along with stomach acid and a churning motion will break the food (especially proteins) down even more. In cases where the body doesn’t produce enough digestive enzymes or the stomach environment is not acidic enough, undigested food will pass further down into the digestive tract and enter the small intestine.

But how do you know if you’ve got enough acidity in your stomach? In a future post, I’ll share information on how you can spot the signs that indicate a lack of stomach acid and what you can do to improve this.

Bile Production

Meanwhile, the liver is stimulated by this process and secretes bile that works to break down fats and further digest food. Problems here are common as bile production can be an issue for many – again, this is an issue we’ll delve into further in future blogs and offer advice on how to enhance bile production to aid this part of digestion.

Absorption & the Small Intestine

The main role of the small intestine is to allow the absorption of nutrients and minerals into the bloodstream through the intestinal wall. But before this happens, our immune system first inspects everything passing through to ensure that it’s safe enough to enter into our blood circulation. When the body is lacking these inspectors, there can be too much intestinal permeability, which can also be a source of problems. The intestinal wall is designed to be permeable enough to allow nutrients to pass through it easily, while preventing toxins. When the wall becomes overly permeable and toxins are able to travel through the wall, this is known as ‘increased intestinal permeability’ or ‘leaky gut’ and can cause many illnesses from allergies to food sensitivities and even autoimmune diseases. The causes can be varied and sometimes will be the results of the issues previously mentioned – such as food not being chewed properly or a lack of stomach acidity/digestive enzymes. The negative effects of this can manifest as food sensitivities and intolerances.

In future blog posts, we’ll explore food allergies, sensitivities and intolerances further. Inflammation, in particular, can be a huge issue and the root cause of many chronic illnesses. For those with a genetic predisposition to increased intestinal permeability, all that is needed for symptoms of an autoimmune disease to appear would be a trigger – such as stress, trauma, chronic insomnia, toxic overload etc. We’ll also talk more about genetic predispositions (how you can figure out what genetic risks you might have and overcome these issues through lifestyle changes) in the not-too distant future.

The Liver & Detoxification

Fortunately, the liver acts as a second point of defence at this stage. Besides its many other roles, it is also our detoxification organ – but rather than viewing it as a safety net against our bad habits and genetic predispositions, we should be mindful that the liver can only take so much and overworking this organ can itself lead to problems. We’ll go into more detail about this and the subject of detoxification in the future as this is another major area of the digestion process where things can go wrong.

Once the nutrients are absorbed from the small intestine, any undigested fibre passes further into the bowel where bacteria will start to break this down into short chain fatty acids – an important fuel source – and through this process, bacteria also produces vitamins (e.g. vitamin K). If we don’t have the right bacteria in the gut, our body is not able to benefit from the effects of these products. Again, we’ll talk more about gut bacteria and learn more in relation to their role in the human body and the many problems that can cause an imbalance of gut bacteria (dysbiosis).


The last step of the digestive system is elimination. It’s a subject that people are often reluctant to talk about despite how common chronic constipation or diarrhea is. Besides the frustration of not being able to eliminate properly, chronic constipation leads to accumulation of toxins in the body, which is the root cause of many conditions. In future blogs we will be talking about ways to improve constipation to achieve better health.

Why is Assimilation So Important?

Assimilation is the most crucial element of Functional Medicine. Without it, it would be impossible for our bodies to survive. And after going through each stage of the process it’s easy to see why; the process of digestion is lengthy and complex. There are lots of different factors that need to work together in harmony to achieve healthy digestion. One seemingly small issue can knock us off balance and has the potential to wreak havoc on our digestive system. That’s why, whatever the problem, treatment that focuses on making assimilation work more efficiently usually results in huge and almost-instant health improvements – not only improving symptoms related to digestion but of many other chronic conditions too.

Written by Andrea Okos