How the gut microbiome helps our body to synthesise vitamins and minerals

---

The gut microbiome is a complex ecosystem consisting of trillions of different types of bacteria, fungi, and other microorganisms that live in our digestive tract.

The gut microbiome is essential to our health, it helps to protect us from chronic disease, helps to boost our immunity and even influences our mental health. One of its most vital roles is aiding in the synthesis and absorption of essential vitamins and minerals, which are crucial for maintaining overall health.

This guide will explore how your gut microbiome helps produce essential nutrients, how an imbalance (gut dysbiosis) can affect nutrient absorption, and how to support your gut for better vitamin and mineral synthesis.

The role of the gut microbiome in nutrient production

A healthy gut microbiome is essential for fermenting fibres that the body cannot digest and producing vital vitamins like B vitamins and vitamin K, which support immunity, metabolism, and overall well-being.

The gut microbiome helps improve the absorption of minerals like magnesium, calcium, and iron by creating favourable gut conditions. While gut bacteria do not convert minerals into bioavailable forms, they enhance absorption by lowering gut pH, breaking down substances that inhibit absorption, and maintaining a healthy gut lining.

A imbalanced gut microbiome can greatly reduce the body's ability to absorb and utilise essential nutrients, even if we consume foods rich in vitamins and minerals. Factors such as a poor diet, chronic stress, and antibiotic use can disrupt gut health, leading to malabsorption, meaning many of these nutrients pass through the digestive system unused. Beneficial gut bacteria play a key role in breaking down food to release essential vitamins, while certain microbes produce enzymes that aid in transporting minerals across the gut lining.

If beneficial gut bacteria are lacking, even a nutrient-dense diet may not be enough to prevent deficiencies. This highlights the importance of maintaining a healthy gut microbiome to ensure that the vitamins and minerals we consume are effectively utilised by the body.

How gut bacteria produce vitamins

Certain gut bacteria can produce essential vitamins that our body needs for metabolic health, immunity and overall well-being. Some of the most important vitamins synthesised by the gut include:

• Vitamin K
• B vitamins (B1, B2, B3, B5, B6, B7, B9, B12)

Vitamin K: essential for blood clotting and bone health

Vitamin K is essential for blood clotting, bone metabolism, and cardiovascular health. The two primary forms of vitamin K include:

• Vitamin K1 (Phylloquinone) – Found in green leafy vegetables like kale and spinach.
• Vitamin K2 (Menaquinone) – Produced by gut bacteria and can also be found in fermented foods like cheese, kefir, yoghurt, natto and sauerkraut, as well as animal sources such as liver, oily fish, chicken, egg yolks, and butter.

Certain strains of gut bacteria, such as Lactococcus lactis, Bifidobacteria, Escherichia coli, and Bacteroides species, produce enzymes that convert vitamin K1 to its active form, vitamin K2. Once converted, vitamin K2 can be absorbed and utilised by the body to support bone health and cardiovascular function.

However, the amount of K2 produced through this process may not be sufficient to fully meet the body’s needs, which is why it's still important to consume foods rich in vitamin K2, such as fermented foods and animal products.

B vitamins (B1, B2, B3, B5, B6, B7, B9, B12)

B vitamins help convert the food we eat into energy and support brain function, skin, hair, and nail health. Many of these are synthesised by our gut bacteria:

• Vitamin B1 (Thiamine) – Beneficial gut bacteria like Bacteroides fragilis, Fusobacterium varium, Prevotella, Bifidobacterium and Lactobacillus can synthesise thiamine, which is necessary for energy metabolism and nervous system function.
• Vitamin B2 (Riboflavin) – Produced by Bacteroidetes, Proteobacteria, Fusobacteria and Lactococcus Lactis. Riboflavin is essential for red blood cell production and energy metabolism.
• Vitamin B3 (Niacin) – Gut bacteria (Bacteroides fragilis, Prevotella copri, Ruminococcus lactaris, Bifidobacterium infantis) can convert tryptophan (an amino acid found in food) into niacin, which supports energy metabolism, skin health, the nervous system and cholesterol regulation.
• Vitamin B5 (Pantothenic Acid) – Enterobacteriaceae species (Escherchia coli and Salmonella typhimurium) help synthesise this vitamin, which is crucial for sex and stress hormone production and energy metabolism.
• Vitamin B6 (Pyridoxine) – Bacteroides fragilis, Prevotella copri, and Bidfidobacterium longum play a role in B6 production, which supports brain health, neurotransmitter function, and immunity.
• Vitamin B7 (Biotin) – Produced by Bacteroides fragilis, Fusobacterium varium, Prevotella copri, and Campylobacter coli, biotin is important for metabolism and healthy skin and hair. However, in cases of gut dysbiosis or bacterial overgrowth (e.g SIBO), harmful bacteria may consume more biotin than they produce, leading to deficiencies.
• Vitamin B9 (Folate) – Many gut bacteria, including Lactobacillus species synthesise folate, which is essential for DNA synthesis and red blood cell production. During pregnancy, folic acid supplements are often recommended because they are more efficiently absorbed than food-derived folate, helping to prevent neural tube defects.
• Vitamin B12 (Cobalamin) – Although gut bacteria (Lactobacillus species and Enterococcus faecium) produce B12, the main source of B12 for humans is dietary intake, as the absorption occurs in the small intestine, which is not where the majority of B12 production by gut bacteria takes place.

How the gut microbiome affects mineral absorption

The gut microbiota plays a vital role in mineral absorption by producing enzymes that break down complex mineral compounds and altering the gut environment to optimise mineral uptake. Some of the key minerals influenced by gut microbes include:

• Iron – Gut bacteria like Lactobacillus, particularly L. plantarum enhance iron absorption by reducing iron to a more absorbable form and promoting a healthy gut lining.
• Calcium – The production of short-chain fatty acids (SCFAs) through the fermentation of dietary fibre helps the body absorb more calcium from the foods we eat.
• Magnesium – A healthy gut lining supports magnesium absorption, which is crucial for muscle function, nerve transmission, and energy production.
• Zinc – Certain gut bacteria, like Lactobacillus and Bifidobacterium improve zinc bioavailability, which is essential for immune function, wound healing, and enzyme activity.

The impact of gut dysbiosis on vitamin and mineral absorption

Beneficial gut bacteria play an important role in the synthesis and absorption of vitamins and minerals. Gut dysbiosis, an imbalance of the gut microbiome, occurs when beneficial bacteria decline and different types of harmful gut bacteria overgrow. This imbalance negatively affects vitamin synthesis and mineral absorption.

Factors that contribute to gut dysbiosis:

• Poor diet (high in processed foods, low in fibre)
• Antibiotic use
• Chronic stress
• Lack of probiotic and prebiotic-rich foods
• Gut infections and inflammatory conditions

When gut bacteria are imbalanced, the production of essential vitamins like vitamin K and B vitamins may decrease, leading to deficiencies. Additionally, impaired mineral absorption can contribute to conditions such as anaemia (iron deficiency) and osteoporosis (calcium deficiency).

Symptoms of poor vitamin and mineral synthesis

When the gut microbiome struggles to synthesise essential vitamins and minerals, it can lead to a range of symptoms that affect overall health including:

• Deficiencies in B vitamins, such as B12 and folate - this can cause fatigue, brain fog, and mood disturbances, while inadequate vitamin K production can contribute to easy bruising and poor blood clotting.
• Impaired mineral absorption, including magnesium and iron - this can lead to muscle cramps, weakness, or anaemia. Gut-related symptoms like bloating, diarrhoea, or constipation often accompany these deficiencies, as an imbalanced microbiome disrupts nutrient metabolism.

Over time, poor vitamin and mineral synthesis can weaken the immune system, impact bone health, and increase inflammation, affecting both digestion and overall wellbeing.

How to measure your gut's ability to synthesise vitamins and minerals

The best way to assess your gut’s ability to synthesise vitamins and minerals is to monitor symptoms such as fatigue, frequent infections, and common digestive issues. These symptoms are your gut’s way of signalling that it isn’t functioning properly.

Additionally, you can take a gut microbiome test. These tests analyse the types and balance of bacteria in your gut, some of which are responsible for vitamin synthesis, our blood test even gives you a score to assess your vitamin synthesis efficiency. Blood tests can also help by checking vitamin and mineral levels in your body, indicating whether your gut is effectively producing and absorbing nutrients.

How to naturally improve your gut health for better nutrient synthesis

Increase your fibre intake

A varied diet rich in prebiotic fibres helps feed beneficial gut bacteria. Good sources include:

• Garlic
• Onions
• Leeks
• Bananas
• Asparagus
• Oats

Include fermented foods

Fermented foods contain beneficial probiotics that help balance gut bacteria and enhance vitamin production. Good options include:

• Yoghurt
• Kefir
• Sauerkraut
• Kimchi
• Miso
• Tempeh

Comprehensive list of foods that are good for gut health.

Saskia's recommendations

The gut microbiome is essential for synthesising key vitamins like vitamin K and B vitamins, as well as enhancing the absorption of vital minerals such as iron, calcium, and magnesium. Maintaining a balanced gut microbiome through diet, probiotics, and healthy lifestyle choices can optimise vitamin and mineral levels, supporting overall health.

If you experience symptoms of vitamin or mineral deficiencies, consider assessing your gut health through microbiome testing and consulting Feel Gut for personalised advice.