When we think of malnutrition, our minds often wander to famine-struck regions or those surviving on poor diets made up of ultra-processed foods. But malnutrition doesn’t only occur when we lack food — it can just as easily happen when our bodies can’t absorb or utilise the food we’re eating. And that’s where gut dysbiosis steps in.
What Is Gut Dysbiosis?
Gut dysbiosis is an imbalance of the microbes in our digestive tract, the trillions of bacteria, yeasts, and other microorganisms forming the gut microbiome. In a healthy gut, beneficial bacteria outnumber the potentially harmful ones. These microbes do far more than just hang around — they help digest food, produce essential vitamins, regulate the immune system, and keep the gut lining strong and healthy.
But when this microbial harmony is disrupted, either by antibiotics, chronic stress, sugar-laden diets, pesticides, or even poor sleep, dysbiosis occurs. The ‘bad bugs’ gain the upper hand, and your digestion and nutrient absorption start to falter.
You Are What You Absorb, Not Just What You Eat
You could be eating a beautifully prepared, traditional, nutrient-dense diet rich in bone broth, liver pâté, vegetables, and dairy, but if your gut is compromised, your body won’t get the full benefit. It’s a bit like putting premium fuel into a car with a clogged fuel line.
Here’s how gut dysbiosis interferes with nutrient absorption:
1. Damaged Gut Lining = Poor Absorption
A healthy gut lining acts as a selective barrier, allowing nutrients through while keeping pathogens and undigested particles out. But dysbiosis can inflame and damage this lining, a condition often referred to as leaky gut (intestinal permeability).
When the gut is inflamed, its ability to absorb nutrients like iron, zinc, magnesium, B vitamins, and fat-soluble vitamins (A, D, E, K) is dramatically reduced. Many people have chronic deficiencies despite a seemingly solid diet, and the root cause is often right there in the gut.
2. Microbes Help Digest and Make Nutrients
Certain beneficial gut bacteria produce vitamins like vitamin K2, B12, folate, and biotin, critical nutrients for everything from energy to fertility. When dysbiosis wipes out these beneficial strains, your internal production line stalls.
Additionally, microbes assist in digesting complex foods. Without their help, you may struggle to fully break down proteins and fats, leading to incomplete digestion and a lack of usable nutrients.
3. Sluggish Digestion and Fermentation
When gut bacteria are imbalanced, digestion slows down. Food sits in the gut longer than it should, leading to fermentation in the wrong places. This causes bloating, gas, constipation, or diarrhoea. These are all signs that digestion and nutrient uptake aren’t functioning well.
Sluggish digestion also means that even traditional foods, such as soaked lentils, sprouted or fermented grains, or slow-cooked stews, may not be properly utilised by the body.
4. Imbalanced ph and Enzyme Function
Your gut bacteria influence ph levels in the small intestine. When harmful bacteria dominate, the ph can become too alkaline or too acidic, either of which affects enzyme function. Digestive enzymes, such as those that break down fats, proteins, and carbohydrates, work best within a specific ph range. When the environment is off, enzymes can’t function optimally, and nutrient breakdown suffers.
5. Increased Nutrient Theft
Pathogenic bacteria and yeasts like Candida albicans feed on nutrients too. When they overgrow, they directly compete with you for critical vitamins and minerals. They’re not just unhelpful house guests — they’re actively robbing your body of nourishment.
Key Nutrient Deficiencies Linked to Gut Dysbiosis
Some of the most common deficiencies seen in clients with dysbiosis include:
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Vitamin A – Needed for skin, eyesight, immune function, and reproductive health.
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Vitamin D – Vital for bones, immune modulation, mood, and hormonal health.
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Vitamin B12 and Folate – Crucial for energy, fertility, and mental health.
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Iron – Commonly low, particularly in women, and affected by gut inflammation and blood loss.
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Zinc – Involved in over 300 enzymatic reactions, and vital for immunity, skin, hormones, and healing.
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Magnesium – Often depleted due to stress, poor absorption, and overgrowth of pathogenic microbes.
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K2 – Essential for directing calcium to the bones rather than the arteries.
So, What Can We Do?
1. Rebuild the Gut Microbiome
Start with food. A traditional nutrient-dense diet naturally supports microbiome diversity and healing:
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Fermented foods: Include small amounts of raw sauerkraut, cultured dairy like kefir or labneh, and fermented garlic or turnips. These introduce beneficial strains and support the terrain.
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Broths and stews: Rich in collagen, gelatin, and minerals that heal the gut lining.
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Animal fats and organ meats: Liver, kidneys, marrow, and butter are rich in fat-soluble vitamins, often depleted in dysbiosis.
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Soaked and sprouted grains/legumes: Easier to digest and more nutrient-accessible. Though when the dysbiosis is quite bad, they may need to be avoided for a while until the gut lining and microbiome have healed.
2. Remove Aggravators
Avoid foods that feed pathogens or inflame the gut:
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Refined sugars
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Industrial seed oils
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Additives and preservatives
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Overconsumption of raw greens or difficult-to-digest vegetables (which can worsen symptoms in some)
3. Support Digestion
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Bitters and herbs: Traditional herbs like mint, cumin, ginger, and black seed (nigella) support digestion.
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Apple cider vinegar or lemon juice in water before meals can gently stimulate stomach acid.
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Proper food combining and chewing thoroughly supports smoother digestion and less fermentation.
4. Tend to the Terrain
Gut healing isn’t just about removing the bad and adding the good — it’s about restoring the whole terrain. Sleep, movement, sunshine, and breathwork are all part of creating an internal environment where the body can thrive.
Final Thoughts
Malnutrition in the context of gut dysbiosis is a hidden epidemic. You might be doing “everything right” with your diet — but if your microbiome is out of balance, your body simply cannot absorb and utilise the nutrients it desperately needs.
The good news? Our bodies are remarkably capable of healing with the right nourishment, support, and time. By addressing gut dysbiosis with a traditional, omnivore diet rooted in ancestral wisdom, we can nourish not just the gut — but the whole self.
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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.