The role of the gut in Vitamin B12 and Iron deficiency (and what to do about it)

With the number of people diagnosed with a Vitamin B12 and Iron deficiency increasing every day, it’s important we address an underlying cause that not many sufferers are aware of: the gut. Too many of those deficient in Iron and/or B12, are simply given supplements, sometimes indefinitely, to try and raise their levels.

What they’re not doing is addressing the reason the deficiency came about in the first place. And for a lot of people, the issue is with their ability to absorb Vitamin B12 in the gastrointestinal tract - a problem that is also often accompanied by IBS-type symptoms. With Vitamin B12 and Iron both essential for almost all functions of the body, a deficiency can contribute to serious long-term ill health.

Here is a summary of what we are going to cover:
> How low levels of Vitamin B12 can cause Iron deficiency anemia
> Symptoms of Vitamin B12 deficiency
> What causes Vitamin B12 deficiency
> The functional lab testing you need to do to uncover the root cause of Vitamin B12 deficiency
> How to correct a Vitamin B12 and Iron deficiency

How Vitamin B12 can Cause Iron Deficiency Anemia

Let’s get this sorted first. Why are we talking about both Vitamin B12 and Iron? Well, it’s because blood loss is one of the primary causes of Iron deficiency. And given B12 is required for the production of red blood cells, a deficiency in Vitamin B12 can lead to a deficiency in Iron. This is why the onset of anemia is often the result of a B12 deficiency rather than an Iron deficiency on its own.

So, if you’ve been diagnosed with low Iron levels, the problem might actually be with your Vitamin B12 levels - our focus for this specific post.

Common Signs and Symptoms of Vitamin B12 Deficiency

Symptoms of a Vitamin B12 deficiency can include:
> Tiredness, fatigue or low energy
> Muscle weakness and aches
> Shortness of breath
> Dizziness or feeling light-headed
> Heart palpitations
> Loss of appetite
> Digestive issues including diarrhoea, cramping and nausea
> Mood changes including depression and anxiety
> Numbness and tingling sensation in hands or feet (peripheral neuropathy)
> Poor concentration, brain fog, memory loss, confusion
> Low Iron levels (explained above).

What Causes Vitamin B12 Deficiency

The causes of Vitamin B12 deficiency generally fall within one of the three following categories:

1. Low dietary intake of Vitamin B12

As our bodies do not make Vitamin B12, we must rely on dietary sources or supplementation. The average adult’s daily requirement is estimated to be 2.4 micrograms a day, with the best dietary sources of B12 coming from animal products.

While plant-based sources of B12 exist, studies have shown they are poorly absorbed and have little to no effect on our B12 blood levels. This presents a challenge for those who follow a vegan and vegetarian way of eating, placing them at risk of Vitamin B12 deficiency.

2. Impaired absorption of Vitamin B12 in the stomach or small intestine

Even with adequate intake of B12, if our body can’t absorb the vitamin then we may still develop a deficiency. The absorption, assimilation, and methylation of B12 is a complex process that involves many steps, as summarised in the diagram below.

Vitamin B12 and Iron Deficiency

Vitamin B12 and Iron Deficiency

Here are the most common reasons for poor absorption of Vitamin B12:

> Low stomach acid - without sufficient HCl and pepsin, the animal proteins that are bound to Vitamin B12 are unable to be digested. This means the B12 is not ‘free’ to bind with other glycoproteins and move through the GI tract for absorption. Anyone with Atrophic Gastritis or Hypochlorhydria as a result of conditions like H. pylori bacterium infection are at particular risk. As is anyone who has been prescribed proton pump inhibitors (PPIs) or acid suppressing medications.

> Exocrine pancreatic insufficiency - without the production of sufficient pancreatic (digestive) enzymes, the body is unable to breakdown the Cobalamin-R complexes in the Duodenum. As a result, the B12 cannot bind with Intrinsic Factor (IF) and make its journey through the small intestine to be absorbed.

> Bacterial dysbiosis and gut infections - high concentration of bacteria in the small intestine (e.g. SIBO) and certain parasites (e.g Giardia) can consume the Vitamin B12 before it is absorbed by the body.

> Surgical resection or disease of the distal ileum - because B12 is absorbed at the lower end of the small intestine, any surgical removal (e.g. weight loss surgery) or an inflammatory condition (e.g. Crohn’s and Celiac disease) that impairs the distal ileum will also impair absorption of Vitamin B12.

3. MTHFR Gene Mutation

Individuals with gene mutations such as MTHFR or MTRR have trouble with the process of methylating B12 into its usable form. So, while the body might absorb sufficient amounts into the blood, it is unable to absorb it into the tissues where it’s ultimately needed. Your Vitamin B12 levels might still be normal or high, however your body just struggles to use it properly.

This has become a relatively hot topic recently and one that many people may be too quick to jump to. Only once you’re eating enough high quality sources of Vitamin B12 and have tested and healed your gut, whether that’s H.pylori, SIBO, parasites or other sources of inflammation, should you be looking to MTHFR gene testing. And if you do decide to complete gene testing early on, make sure you’re onto the gut testing as well.

The functional lab testing you need to do to uncover the root cause of Vitamin B12 Deficiency

While you might have already done the standard blood test to identify low levels of Vitamin B12 and Iron, the important testing you need now is to find out the underlying root cause. These are a comprehensive Stool Test, Organic Acids Test and/or SIBO Breath Test.

If none of these tests reveal underlying gut dysfunction and/or you have already healed your gut, that’s when it’s important to look to MTHFR gene testing.

How to correct a Vitamin B12 and Iron Deficiency

1. Dietary Sources High in Vitamin B12

As discussed above, the average adult’s daily requirement is 2.4 micrograms a day, with the best dietary sources of Vitamin B12 coming from animal products. And although the exact rate of absorbability depends on a person’s digestive health, here are the top food sources of B12:
> Beef and chicken liver
> Salmon
> Herring
> Mackerel
> Sardines
> Tuna
> Trout
> Organic greek yoghurt
> Turkey
> Beef
> Lamb
> Eggs

2. Heal the gut to improve Vitamin B12 absorption

Given the importance of a healthy and well-functioning GI tract for the absorption of Vitamin B12, healing your gut could be the key to healing a B12 deficiency. The most common gut related conditions I see that impair B12 absorption, are:
> H. pylori - lowers stomach acidity and the animal proteins that are bound to Vitamin B12 are unable to be digested.
> SIBO - bacterial overgrowths in the small intestine can consume the Vitamin B12 before it is absorbed by the body.
> Parasites - infections like Giardia can also compete with the body for the absorption of Vitamin B12.

If you have a Vitamin B12 deficiency and also suffer from GI related symptoms then it is advisable to have a practitioner order some functional lab tests to identify potential gut infections or other imbalances.

Only once you have identified the underlying cause of the Vitamin B12 malabsorption (and deficiency) can you work to eradicate the infection and heal the lining of the gut. While healing the gut, I often recommend supplementing with HCl and digestive enzymes to help B12 absorption from food sources.

3. Supplement Vitamin B12

For those with permanent B12 malabsorption, such as individuals with MTHFR gene mutations, vegans/vegetarians, IBD or ileum resection, Vitamin B12 supplementation is generally recommended.

For anyone healing their gut to correct a B12 deficiency, short-term supplementation might still be advisable depending on your current B12 levels and the amount of gut healing that is required.

When looking for B12 supplements, be sure to look for it in the form of methylcobalamin, rather than cyanocobalamin. This Methyl-B12 form is typically the easiest for the body to absorb and utilise, giving the biggest impact on your B12 levels. There are three main ways you can get your B12 supplementation:
> Orally in capsule form - easiest to find at the store or available on Amazon here (USA) or iHerb here (Australia).
> Sublingual drops - recommended for those with SIBO or other gut infections or imbalances that are affecting absorption. Normally available via practitioners or available on Amazon here (USA).
> Injections - recommended for more serious cases of deficiency including pernicious anemia and severe depletion causing neurological disorders.


If you suspect you have a Vitamin B12 and/or Iron deficiency, the first step is to get tested. If you are deficient in B12, step two is to identify the underlying mechanism or cause of your deficiency. Once the root cause is identified, the appropriate form of supplementation (oral, sublingual or injection), dosages and length of treatment can be determined, as well as any gut healing and rebalancing that needs to occur to heal the root cause. I hope you found this post useful and continue to work towards vibrant health, minus the B12 deficiency.

Healing the gut is a journey. If you are ready to begin yours, please head to the Work With Me page to learn more about how I work online with clients in many countries to test for and treat the many root causes of IBS symptoms and other GI conditions.

Note: Affiliate links for iHerb and Amazon have been included in this blog post. These do not adversely affect the price you pay.