You eat well.
You take your supplements.
You may even be eating foods rich in B12 and getting plenty of sunshine.
And yet your blood test comes back:
Vitamin B12: LOW. Vitamin D: LOW.
So you take more.
And then… a few months later, they're low again.
Sound familiar?
We tend to think of nutrient deficiencies as a simple equation:
Eat the nutrient → absorb the nutrient → levels go up.
But your digestive system is much more complicated than that.
Before a nutrient can reach your bloodstream, it has to survive digestion, be released from food, pass through several stages of processing, and — most importantly —be absorbed by the right part of your gut.
This is why your gut health can have a surprisingly important influence on your nutrient status.
🧬You can eat a nutrient without absorbing it
This is one of the most important concepts in nutrition.
Nutrient intake ≠ nutrient absorption.
You could technically consume enough of a vitamin or mineral and still have low levels if something is interfering with digestion or absorption.
And several parts of your digestive system are involved.
Think:
Stomach → pancreas → bile → small intestine → intestinal lining → bloodstream
Every step matters.
🧪First stop: your stomach
Your stomach isn't just a storage bag for food.
It produces hydrochloric acid (stomach acid), which plays an important role in digestion.
And B12 is a particularly interesting example.
Vitamin B12 in food is generally bound to proteins.
Stomach acid and digestive enzymes help release B12 from food proteins.
B12 then binds to proteins called R-proteins, and later, further along the digestive tract, it eventually binds to intrinsic factor— a protein produced by cells in the stomach.
The B12–intrinsic factor complex is then absorbed in the terminal ileum, the last part of the small intestine.
So B12 absorption isn't simply:
“Eat B12 → absorb B12.”
It's a multi-step process.
🟠Where does low stomach acid come in?
This is where things get interesting.
As we get older, some people produce less stomach acid.
Certain stomach conditions can also affect acid production.
And some medications — particularly proton pump inhibitors(PPIs)and other acid-suppressing medicines — deliberately reduce stomach acid.
These medicines can be extremely useful and appropriate when medically indicated.
But long-term acid suppression can affect the absorption of some nutrients, including food-bound B12.
Why?
Because if less stomach acid is available, it may be harder to release B12 from the proteins in food.
This doesn't mean:
“Antacids cause B12 deficiency.”
It means thatlong-term acid-suppressing medication is one factor doctors may consider when evaluating unexplained B12 deficiency.
And that's a very different — and much more useful — way of thinking about it.
💊What about antacids?
This deserves its own conversation because millions of people take them.
Antacids and acid-suppressing medicines aren't all the same.
There are:
● Simple antacids that neutralize stomach acid ● H2 blockers that reduce acid production ● PPIs that more strongly suppress acid production
Short-term use is generally very different from long-term, regular use.
With prolonged acid suppression, studies have found associations with deficiencies or altered absorption of nutrients such as B12, magnesium, and iron in some people.
That doesn't mean you should stop your medication.
Please don't.
If you're taking a PPI or other acid-suppressing medication regularly and have unexplained nutrient deficiencies, it's worth discussing the combination with your doctor.
The answer may be as simple as monitoring your levels, reviewing the medication, and looking for another cause.
🩸B12 isn't just about stomach acid
This is where the gut story gets even bigger.
Even after B12 survives the stomach, it still needs:
Intrinsic factor → healthy small intestine → functioning terminal ileum
Conditions affecting the stomach or small intestine can interfere with this process.
Examples include:
H. pylori infection
H. pylori can cause chronic inflammation of the stomach lining and, in some people, contribute to impaired B12 absorption.
Atrophic gastritis
Damage to the stomach lining can reduce the cells responsible for producing intrinsic factor.
Celiac disease
Damage to the small-intestinal lining can interfere with nutrient absorption.
Crohn's disease
If the terminal ileum is affected, B12 absorption can be impaired.
Certain gastrointestinal surgeries
Procedures that remove or bypass parts of the stomach or small intestine can dramatically change nutrient absorption.
So sometimes a low B12 level isn't really a“B12 intake problem.”
It's an absorption problem.
☀️And then there's Vitamin D
Vitamin D has a completely different absorption story.
Unlike B12, vitamin D is fat-soluble.
That means your body needs normal fat digestion and absorption to efficiently absorb vitamin D from food and supplements.
And that brings us to another set of digestive players:
Bile + pancreatic enzymes + healthy small intestine
Your liver makes bile.
Your gallbladder stores and releases it.
Bile helps emulsify dietary fat so that your digestive enzymes can break it down and your intestine can absorb the resulting fat and fat-soluble compounds.
And vitamin D belongs to that fat-soluble group.
So problems with fat digestion or fat absorption can potentially affect vitamin D absorption.
🟢Your liver and gallbladder are part of the nutrient story too
This is something people rarely think about.
When we say “gut health,” we often mean:
bloating + constipation + diarrhoea.
But digestion is an entire system.
Your:
Liver → makes bile Gallbladder → stores and releases bile Pancreas → produces digestive enzymes Small intestine → absorbs nutrients
If something goes wrong with fat digestion or absorption, you can potentially have difficulty absorbing vitamins A, D, E, and K.
This is why persistent greasy or oily stools, very pale stools, unexplained weight loss, or chronic diarrhoea deserve medical evaluation rather than simply adding another supplement.
🦠What about the gut microbiome?
Your gut microbes interact with the food you eat and produce a huge variety of metabolites.
They're particularly important for fermentation of dietary fibre and production of short-chain fatty acids, which support the intestinal environment.
But let's not oversimplify this into:
“Bad gut bacteria = vitamin D deficiency.”
Human nutrient status is much more complicated.
For B12 and vitamin D, the bigger practical questions are usually:
Are you consuming enough?
Are you digesting it properly?
Are you absorbing it properly?
Is a medication interfering?
Is there an underlying gastrointestinal condition?
Those questions are much more useful than simply blaming your microbiome.
🚨Why repeatedly supplementing isn't always the answer
If your B12 or vitamin D keeps coming back low, don't just keep increasing your supplement dose indefinitely.
Ask:
1. Am I actually getting enough?
Diet matters.
2. Could I have an absorption issue?
Especially if multiple nutrients are low.
3. Am I taking acid-suppressing medication regularly?
This is particularly relevant for B12 and some other nutrients.
4. Do I have gastrointestinal symptoms?
Persistent diarrhoea, bloating, abdominal pain, unexplained weight loss or greasy stools can be clues that deserve investigation.
5. Could there be an underlying condition?
Depending on the situation, doctors may consider conditions such as celiac disease, autoimmune gastritis, H. pylori infection, inflammatory bowel disease or pancreatic/biliary disorders.
🌿So how do you support nutrient absorption?
You don't need a complicated “gut detox.”
Start with the fundamentals.
Eat a diverse whole-food diet
Different foods provide different nutrients, fibre and plant compounds.
Get enough protein
Adequate protein supports overall nutrition and provides amino acids needed for many physiological processes.
Eat enough healthy fat
Fat is necessary for absorption of fat-soluble vitamins.
Think nuts, seeds, dairy if tolerated, olive oil, avocado, ghee and other minimally processed sources.
Eat fibre-rich plant foods
Vegetables, fruits, legumes, whole grains, nuts and seeds support a diverse diet and healthy intestinal environment.
Don't routinely overuse acid-suppressing medication
But never stop prescribed medication without speaking to your doctor.
If you're using antacids or PPIs regularly for months or years, discuss whether continued treatment is necessary and whether nutrient monitoring makes sense.
Investigate persistent digestive symptoms
Don't normalize chronic bloating, diarrhoea, constipation, reflux or unexplained food intolerance indefinitely.
Your gut is giving you information.
🧡Your nutrient levels tell a story
A blood test that says“B12 = low” or“Vitamin D = low” is giving you a number.
But sometimes, the more interesting question is:
Why?
Maybe you're simply not consuming enough.
Maybe you need supplementation.
Maybe you aren't absorbing it efficiently.
Maybe your stomach isn't producing enough acid.
Maybe you're taking an acid-suppressing medication.
Maybe your stomach lining is inflamed.
Maybe your small intestine isn't absorbing nutrients properly.
Maybe your bile or pancreatic function needs to be investigated.
The nutrient is the endpoint. Your digestive system may be part of the journey.
And that is why at MOSHA, we don't look at gut health as simply “bloating” or “constipation.”
Your digestive system sits at the centre of digestion, absorption and nutrition.
So if your nutrient levels keep falling despite doing everything “right,” don't just ask:
“Which supplement should I take?”
Also ask:
“Am I absorbing what I'm taking?”
That's where the real gut-health conversation begins.🌿