When we talk about nourishment, it’s easy to focus solely on what’s on our plate: the rich broths, vibrant ferments, organ meats, raw dairy, and mineral-rich vegetables. But true nourishment doesn’t end with eating. It continues deep within, where the magic of digestion and absorption unfolds—particularly in the gut. Even the most nutrient-dense meals can leave the body deficient without a well-functioning gut.
In this post, I’ll explore how gut health directly affects your ability to absorb key vitamins and minerals, why deficiencies often stem from gut dysbiosis, and how we can restore balance using traditional, time-honoured dietary approaches.
The Gut as a Gatekeeper of Nutrients
The gastrointestinal tract is not just a passageway; it’s a dynamic, intelligent system that digests, assimilates, and regulates the nutrients from the foods we consume. The small intestine is where the majority of nutrient absorption occurs, and it relies heavily on a well-balanced gut microbiome, strong digestive secretions, and an intact mucosal lining.
When the gut is in good health, beneficial microbes help synthesise certain nutrients (like vitamin K2 and B vitamins), break down complex foods for easier absorption, and support a healthy gut lining to prevent leakage and inflammation. But when the gut is imbalanced, what we call gut dysbiosis, this harmony is disrupted.
What is Gut Dysbiosis?
Gut dysbiosis refers to an imbalance between beneficial microbes and opportunistic or pathogenic ones in the digestive tract. This imbalance can be caused by:
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Antibiotic use (even from food residues in non-organic meats)
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A highly refined, sugar-laden, industrialised diet
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Chronic stress
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Overuse of sanitising products
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Exposure to environmental toxins
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Birth by C-section or lack of breastfeeding
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Low stomach acid or enzyme production
When this microbial imbalance takes hold, nutrient absorption suffers—and the consequences can be wide-reaching.
How Gut Dysbiosis Impairs Nutrient Absorption
Let’s look at how specific deficiencies can stem from gut issues:
1. Fat-Soluble Vitamins (A, D, E, K2)
These nutrients require adequate fat digestion and bile production for proper absorption. When dysbiosis inflames the gut lining or disrupts bile flow, the absorption of fat-soluble vitamins plummets. Vitamin A and D, both critical for immunity and hormonal health, often become deficient, even in those eating liver, pastured butter, or taking cod liver oil.
Moreover, beneficial gut bacteria are involved in producing vitamin K2, which is essential for calcium metabolism and bone strength. A disrupted microbiome means less K2 production, increasing risks of osteoporosis, tooth decay, and calcification in arteries.
2. B-Vitamins (especially B12, B6, and B9/Folate)
B vitamins are co-factors in everything from energy metabolism to brain health. Gut dysbiosis can impair their absorption in several ways:
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Damage to the stomach lining or insufficient stomach acid (often due to H. pylori or chronic stress) reduces B12 absorption.
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Imbalanced flora fails to synthesise sufficient B9/folate.
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Inflammation in the small intestine (common in leaky gut or SIBO) hinders B-vitamin uptake overall.
3. Iron, Zinc, Magnesium & Calcium
These essential minerals are absorbed in different parts of the intestine, and they depend on both proper pH and a healthy mucosal surface. With dysbiosis:
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Iron absorption drops, especially in women, leading to fatigue and low immunity.
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Zinc becomes depleted, affecting everything from taste to immune function and skin health.
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Magnesium deficiency contributes to muscle cramps, poor sleep, and anxiety.
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Calcium is poorly absorbed without enough vitamin D, K2, and healthy gut flora.
Even if you’re eating oysters, mineral-rich bone broths, and raw dairy, a compromised gut can prevent your body from utilising them.
Healing the Gut: The Traditional Nutrient-Dense Approach
To truly address vitamin and mineral deficiencies, we must support the gut, not just with supplements but by restoring its natural environment. Here’s how:
1. Eat Fermented Foods Daily
Raw sauerkraut, fermented carrots with spices, kefir (from raw milk), and fermented beetroot not only introduce beneficial bacteria but also enhance digestion and support enzyme activity.
2. Emphasise Bone Broths and Gelatinous Cuts
Broths from lamb neck, beef shin, or chicken feet nourish the gut lining, reduce inflammation, and support the regeneration of enterocytes (the cells lining the gut wall).
3. Include Healthy Fats
Butter from grass-fed cows, lamb fat, pastured duck fat, and olive oil support the absorption of fat-soluble vitamins. They also support bile production, which is critical for proper fat digestion.
4. Prioritise Organ Meats
Liver, heart, and kidney are some of the most concentrated sources of B vitamins, iron, and zinc. Liver pâté with caraway seeds or lamb liver sautéed with garlic and parsley is both delicious and medicinal.
5. Support Stomach Acid and Digestive Fire
Begin meals with a spoonful of fermented vegetables or drink a little raw apple cider vinegar in water (if tolerated) before meals. Bitter herbs and a calm eating environment also stimulate digestive secretions.
6. Avoid Gut Irritants
Cut out refined sugars, industrial seed oils, and overly processed foods. Avoid synthetic supplements unless guided—they can often irritate the gut further.
A Note on Testing and Supplements
Sometimes, functional testing can help identify specific deficiencies or gut imbalances (like low stomach acid, SIBO, or low microbial diversity). If supplementation is needed, choose whole-food based options, such as desiccated liver capsules or mineral drops derived from sea water.
But supplements alone can’t replace the power of a nourishing traditional diet. As Sally Fallon often reminds us, “You can’t supplement your way out of a bad diet.”
Conclusion
Healing from deficiencies isn’t just about piling on more nutrients—it’s about creating the inner conditions where those nutrients can be received, processed, and utilised. That’s the beauty of focusing on the gut. When we restore the microbial balance, support digestion, and eat according to ancestral wisdom, the body begins to absorb and thrive again.
If you’re dealing with persistent deficiencies, it’s time to look within, not just at what you’re eating but how your body is receiving it.
And the healing journey? It begins in the gut.
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Disclaimer: The content of this blog post is for informational purposes only and is not intended as medical advice. While I strive to provide accurate, well-researched, and up-to-date information, I am not a licensed medical professional. The insights shared here are based on personal research and experience. I encourage you to conduct your own research and consult a qualified healthcare provider before making any health-related decisions. Your well-being is important, and any actions taken based on the information in this blog are solely at your own discretion and risk.