The purpose of this article is to introduce you the concept of B vitamin metabolism, the effect the immune system can have in interfering with your B vitamin metabolism, how B vitamins impact detoxification and how problems metabolizing B vitamins aggravate certain conditions.

We all need and use B vitamins daily for survival. However, when we suffer from a chronic disease or inflammatory disorder such as Autism, Asperger’s  syndrome, ADD, ADHD, OCD, depression, PMS, seasonal allergies, food allergies, environmental sensitivities, arthritis, acid reflux, diabetes, chronic fatigue, fibromyalgia, lyme disease, eczema, hives, itchy skin, brain fog, developmental delay disorders, chronic sinusitis, recurrent ear infections, irritable bowel, Crohn’s disease, celiac sprue, heavy metal toxicity, toxic teeth, chronic viral infections, mood disorders, and/or insomnia, our metabolism of B vitamins may not be functioning correctly. Traditional medicine looks at the levels of B vitamins in a patient and makes a HUGE ASSUMPTION that if the level of a vitamin is low, it is because they are deficient in that vitamin AND that they are not taking enough of that vitamin from food or supplementation. This is not necessarily true! It completely ignores the issue of how the body metabolizes B vitamins and how the immune system can become triggered to block the body’s synthesis and degradation of B vitamin metabolites.


If your immune system recognizes a B vitamin such as B12, then it blocks the usage of that vitamin to various degrees by treating it as a foreign invader. The immune system may blocking its usage, to various degrees, eliminating it from your body and making it appear as if you are deficient in that vitamin. The degree of immune interference with that vitamin varies depending on the degree and type of inflammation that patient is suffering from.  If the immune system recognizes a metabolite or a number of metabolites in the synthesis or degradation of B vitamins, then you will have a proportional inhibition either in the synthesis of a B vitamin or degradation in that vitamin.


The liver performs over 40,000 metabolic processes in the body. A handful of these involve detoxification. The most significant pathway is called the methylation pathway for many reasons. This pathway is new on the frontier of understanding our genetic and metabolic connection to detoxification. Certain genetic variations in this pathway make it more difficult for some individuals to bind and excrete toxins. For purposes of this article, B6 and B12 and 5-tetra-hydroxy-folate are essential to run this pathway. Think of them as key ingredients in a recipe. Without them, the bread does not rise and you do not get the desired result. If your immune system interferes with the usage of an ingredient needed to make a B vitamin such as B12, then the availability of that vitamin to fuel the detoxification pathway will be hindered in direct proportion to the degree of immune system interference. If your immune system hinders the degradation of a B vitamin in the liver, then the toxic load to your liver increases and the B vitamin metabolites act as fuel to increase inflammation to specific body receptor sites such as the brain, nerve tissue and neurotransmitter synthesis, and skin.

The most significant challenges seen involving the usage of B vitamins occurs in the autism spectrum of disorders. The child’s immune system is on hyper alert and with various treatment programs, large quantities of B vitamins are given to the child by many doctors. The parents may begin to see an increase in symptoms when B vitamin dosage is increased. This can also occur when the level of glutathione or other heavy metal chelators are given to the child. These chelators increase the body’s demand for key B vitamins and can aggravate immune system interference with B vitamin synthesis and degradation in the body, sometimes derailing the body’s ability to use B vitamins. These children do need more B vitamins when pushed to detoxify but their immune system does not allow for this increased demand. This occurs in addition to any genetic defects in their detoxification pathways called SNPs.

In other autism spectrum cases, increasing the dosage of B vitamins increases the neurological inflammation present in the brains of these children and their neurological symptoms increase. What has also been known to occur is that the immune sensitivity to the B vitamin is also linked to an immune recognition with a neurotransmitter(s). As a result you see, more aggression, more head banging, & shorter attention span. They seem to regress. This is a huge sign that there is a metabolic block to pushing their body to metabolize more B vitamins.

Many other inflammatory condition involve this same mechanism of action in preventing a patient from taking and using their B vitamins. The more the inflammation, the worse the reactivity can be to the B vitamin. As a result skin conditions can worsen in eczema and hives. Chronic fatigue and fibromyalgia patients can suffer more fatigue and increased pain and body aches. Those with toxic teeth or heavy metal toxicity can suffer body stiffness, body pain, tight muscles, headaches, even to the point of migraine. The frequency of irritable bowel and other digestive disorders can peak.

Immune Matrix has a proprietary protocol for testing and treating these complex detoxification pathways. The result is that the patient is able to begin to use B vitamins. Smaller dosages are needed, taxing the liver less. Neurotransmitter synthesis and performance improves. Heavy metal excretion improves. Behavior of the child begins to improve such that teachers begin to take note and ask the parent what they are doing to change their child. Laboratory values for B vitamins normalize. Immune cell interference on detoxification pathways declines and patients are able to excrete toxins without complications. Their excretion of heavy metals increases. Mental clarity and energy begin to improve from improved levels of B vitamin metabolism.

Any chronic inflammatory condition can be aggravated by immune cell recognition of B vitamin metabolites. This results in your being deficient in your usage of B vitamins and causes you to become more toxic from taking B vitamins because they cannot be eliminated from the liver as easily.

Most B vitamins on the market are synthetic. Synthetic B vitamins are a molecular opposite of the natural form we need in our body. As a result, this synthetic B vitamin has to be “degraded”, broken down in the liver. It then must be converted to a natural form of B vitamin. This conversion is never 100%. Therefore, the conversion of synthetic B vitamins always increases one’s toxic load. If you have immune cell interference in the conversion, either in synthesis or degradation, then your toxic burden increases. Your tolerance to B vitamins decreases! This is why many people react to their vitamins!

Chronic inflammatory conditions such as autism, arthritis, eczema, chronic fatigue, fibromyalgia, Hashimoto’s thyroiditis, Chron’s disease, celiac disease, psoriasis, ADD, ADHD, all tend to need more B vitamins. Inflammation depletes the bio-availability of B vitamins. Stress from inflammation depletes the bio-availability of B vitamins. Increased toxicity depletes the body of B vitamins. Life stresses affect these individuals more, because of their inefficient B vitamin metabolism. Diet also depletes the body B vitamins! Especially coffee, nuts, gelatin, pineapple, chocolate. Chronic viral infections deplete the body of B vitamins. Now you can see how the body is drained of B vitamins necessary for efficient detoxification. This does not even allow for the usage of B vitamins for neurotransmitters and nerve repair, stress management, and skin repair!

B vitamins are essential to:

1)     Detoxify efficiently

2)     To make neurotransmitters

3)     To repair nerve cells and neurons in the brain

4)     To manage stress

5)     To repair skin

When your immune system interferes with B vitamin degradation, synthesis or detoxification:

1)     B vitamin metabolites accumulate in the liver increasing your toxicity

2)     Hinder efficient detoxification of heavy metals & other toxins

3)     Hinder repair of brain cells, allowing toxins to aggravate the brain

4)     Hinder repair of nerve tissue in the body, allowing toxins to aggravate nerves in the body. This increases irritable bowel, increases pain sensation, numbness and tingling in the limbs, and aggravates insomnia, irritability, and mood.

5)     You become more reactive to taking B vitamin supplements. You can have rashes, hives, feel shaky, heart pounding, irritable, etc.

6)     You become unable to process other vitamins, tinctures, drugs, and supplements, because of increasing toxic load and inefficient detoxification metabolism. Some patients are unable to take what their doctors give them for this very reason.


1)     B vitamins are best absorbed when in the natural form from foods. In the United States those supplements that are not synthetic but food based have to list the foods on the bottle to show the basis in which the vitamins are extracted.

2)     It helps to find out your genetic SNPs for the methylation pathway. You can contact Immune Matrix at 408-262-6900 to find out how you can be tested. This will help to determine whether you can handle methyl donors or need a different type of B vitamin supplementation.

3)     You can be tested at www.immunematrix.com and have those pathways treated to make your methylation pathway more efficient. Immune Matrix will also determine if there is a cross-reaction going on between B vitamins, neurotransmitters and methylation, the classic triad that aggravates chronic inflammatory conditions.

4)     Try to avoid a synthetic B vitamin and in its place, take a sublingual B12 and 5-tetra-hydroxyfolate. By limiting your B vitamins to these two for a period 30-60 days you can give your immune system a break and help provide the key detoxification catalysts. Be sure to take some form of magnesium (preferably with a mineral supplement that contains molybdenum). These two additional minerals are key ingredients that drive the methylation pathway making efficient detoxification possible.

5)     Take smaller doses of your prescribed supplements and more frequently during the day if possible. Avoid taking B vitamins after 3p.m. as this can disturb your sleep.

6)     Take one activated charcoal at night before bedtime to help absorb toxins the body is unable to bind. This minimizes the side effect one can feel from reacting to toxins that the body is unable to bind and excrete. Activated charcoal can cause constipation, therefore, take only one and only as needed.

7)     Drink more water to help flush toxins through your bowels and urinary track.

As you are now beginning to understand, taking a vitamin because your lab test says you are deficient often does not take care of the deficiency. The body has a wisdom WHY it is deficient – usually there is a metabolic hindrance to using that substance. That metabolic hindrance can be from a genetic defect that can be bypassed with proper supplementation to side pass the defect. That hindrance can be aggravated by immune sensitivities to the vitamin or its metabolite. That hindrance can also be aggravated by immune cross-reactions with neurotransmitters and other metabolites which hinder B vitamin metabolism, excretion, or interaction with other neurotransmitters in the brain and nervous system. The dynamics are interrelated and therefore consulting with a health care professional experienced in reading labs in light of the dynamics of immune sensitivities and how they relate to one’s core detoxification pathways are often necessary with a more chronic inflammatory condition.

Please note:
Information on this site is provided for informational purposes only and is not intended as a substitute for the advice provided by your physician or other healthcare professional. You should not use the information on this site for diagnosing or treating a health problem or disease, or prescribing any medication or other treatment.

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  2. I have been  followed by a liver specialist due to a gitt level of 410
  3.  I break out from foods fortified with B vitamins.
  4. Is this related to the same metabolism problem?


I have high serum levels of B6 but take little to none in supplement form at this point.  I used to take more (50 mg per day maybe) but have been advised by neurologists to not take any in the hopes of stopping or reversing a worsening sensory neuropathy (numbness).  I am at my wits end!  Why they aren't interested in the reason behind this problem with excreting B6 is beyond me.  This article was very interesting though I have the opposite problem... I think.


Me too! Still searching for the answer


@riswid @kellyj12 My wife has the same thing going on where Serum levels are high and she is also experiencing some peripheral neuropathy, but the symptomatic is actually that of B6 deficiency. A good explanation that we found is in the difference of Pyridoxine - which is usually what is supplemented - and P5P which is the active form of Vitamin B6. The serum test will most likely be picking up Pyridoxine, which can be elevated while the body actually lacks in P5P, the active form.

There are a number of articles out there explaining the conversion and the co-factors necessary (like the active form of B2). Here is one I found quickly: http://www.terrytalksnutrition.com/health-articles/the-life-saving-value-of-pyridoxal-5-phosphate-p5p-and-magnesium/

The Article mentions, that there are a number of individuals that can not convert Pyridoxin to P5P or that the conversion is at least greatly slowed. I read about a study in which only about a third of the participants were able to raise their P5P level by supplementing with Pyridoxine.

A solution can be to supplement with the active form which is P5P. 

Something that might also be of interest to you is a metabolic disorder called Pyroluria (also known as HPU or Kryptopyrole or Pyrrole disorder). There is some good information out there by a Lady called Trudy Scott.


I only used P5P and still B6 toxic.


(apologies for the duplicate!)

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Anna Manayan

Anna Manayan