What vitamins are produced by microbes?

December 11, 2025 •

4 min read

Recent genome annotation studies suggest that up to 65% of human gut commensal microorganisms have the ability to produce at least one type of B vitamin. The question of what vitamins are produced by microbes uncovers a vital and complex relationship between our health and the microbial world, spanning our gut, fermented foods, and industrial processes.

Quick Summary

This article details the specific vitamins synthesized by microbes in the human gut and through industrial fermentation. It outlines the health benefits and discusses how diet and environment influence microbial vitamin synthesis.

Key Points

Exclusive B12 Production: Vitamin B12 is synthesized exclusively by certain bacteria and archaea, and is not produced by plants or animals.
Gut Microbes Produce B and K2: Commensal bacteria in the human large intestine, including Bacteroides and Bifidobacterium species, produce significant amounts of B-complex vitamins and vitamin K2.
Bioavailability Varies: The absorption and utilization of microbially produced vitamins by the human host can be limited, especially for those synthesized in the colon, as efficient absorption often occurs earlier in the digestive tract.
Industrial Production for Supplements: Large-scale vitamin production for supplements, fortified foods, and animal feed relies on optimized microbial fermentation using high-yield bacterial and fungal strains.
Diet and Drugs Impact Synthesis: The specific vitamins and quantities produced by the gut microbiome are influenced by diet, antibiotic use, and overall gut health, demonstrating a dynamic and complex relationship.
Fermented Foods are a Source: Foods fermented by bacteria, such as natto and some cheeses, contain valuable amounts of microbially synthesized vitamins, especially vitamin K2.

The Microbial Vitamin Factory

Microorganisms are not just passive inhabitants of our environment; they are active biochemical factories, producing a wide array of compounds, including essential vitamins. This process, known as microbial synthesis, is vital for the ecosystem and for human health, both within our bodies and in industrial applications. While humans must acquire most vitamins through diet, certain microbes, especially in our gut, contribute significantly to our nutritional status.

Vitamins Produced by Microbes

The list of vitamins produced by microbes is extensive, covering a wide range of functions from energy metabolism to blood clotting. Some of the most notable examples include:

Vitamin B12 (Cobalamin): This is perhaps the most famous example, as it is synthesized exclusively by certain bacteria and archaea. Neither plants nor animals can produce it. Humans acquire B12 from animal-source foods, where it has been transferred and accumulated through microbial interactions.
Vitamin K2 (Menaquinones): Primarily of microbial origin, various forms of K2 (MK-n) are synthesized by gut bacteria, notably species within the genera Bacteroides and Lactobacillus. These microbes synthesize K2 as part of their energy metabolism.
B-Complex Vitamins: A wide variety of B vitamins are produced by gut and fermenting microbes, including:
- Riboflavin (B2): Produced by bacteria like Bacillus subtilis and fungi such as Ashbya gossypii, which are used for industrial production.
- Biotin (B7): A vital cofactor synthesized by bacteria including Bacteroides and Fusobacterium species in the gut.
- Folate (B9): Certain species of Lactobacillus and Bifidobacterium are known folate producers, contributing to the host's folate status.
- Thiamine (B1): Some intestinal bacteria, like Prevotella and Desulfovibrio, possess the capacity for thiamine biosynthesis.
- Niacin (B3): Synthesized by bacteria in the gut, with certain species like Bacteroides fragilis and Ruminococcus lactaris possessing the necessary pathways.
Ergocalciferol (Vitamin D2): Certain fungi and yeasts, such as Saccharomyces cerevisiae, can produce ergosterol, which can be converted to vitamin D2 upon UV exposure.

The Role of Gut Microbes in Vitamin Synthesis

The human gastrointestinal tract is a bustling ecosystem where symbiotic relationships play a crucial role in our nutrition. The trillions of bacteria, fungi, and other microorganisms living in our colon produce an impressive range of vitamins. This localized production helps maintain a healthy gut and can supplement the body's dietary intake, especially for certain B and K vitamins.

However, the extent to which we can absorb and utilize these microbially produced vitamins is a subject of ongoing research. For instance, most absorption occurs in the small intestine, but many of the producing microbes reside in the large intestine (colon). For some fat-soluble vitamins like K2, absorption from the colon is less efficient than from the small intestine, potentially limiting the benefit to the host.

The Impact of Diet and Antibiotics

The composition of the gut microbiome, and consequently its vitamin synthesis capabilities, can be profoundly affected by external factors. A person's diet is a primary driver, with different dietary components favoring the growth of certain microbial species over others. For example, diets high in prebiotics can stimulate the growth of beneficial bacteria, including some vitamin producers. Conversely, long-term use of broad-spectrum antibiotics can kill off the delicate balance of gut flora, leading to reduced vitamin synthesis and potentially triggering deficiencies.

Comparing Microbial Vitamin Production: Gut vs. Industrial

Microbial production of vitamins occurs naturally in our bodies but is also harnessed on an industrial scale. The following table highlights the key differences and applications.


Feature	Gut Microbiota Production	Industrial Microbial Fermentation
Purpose	Symbiotic benefit for host and other microbes	Commercial production for supplements, fortified foods, and animal feed
Location	Primarily the large intestine (colon)	Bioreactors and other controlled environments
Contributing Organisms	Diverse community of commensal bacteria (e.g., Bacteroides, Bifidobacterium)	Specially selected and engineered high-yield strains (e.g., Propionibacterium, Bacillus, Ashbya)
Vitamins Produced	B-complex vitamins, vitamin K2	B-complex vitamins, vitamin C, vitamin D2, vitamin K2
Scale	Varies greatly between individuals; often insufficient to meet daily needs	Large-scale, optimized to meet global demands
Absorption for Host	Limited absorption in some cases; can benefit other microbes in the gut	Purified products are readily absorbed when ingested

Fermented Foods and Probiotics as Microbial Vitamin Sources

Beyond our gut, fermentation processes are a significant source of microbially produced vitamins. Fermented foods like cheese, yogurt, and especially natto (fermented soybeans) contain valuable amounts of vitamins, particularly K2. The specific vitamin content can vary depending on the bacterial or fungal strains used in the fermentation process. Probiotic supplements, which contain live microorganisms, are also being explored for their potential to deliver certain vitamins directly to the gut, thereby enhancing the host's nutritional status. Research indicates that some probiotic strains of Lactobacillus and Bifidobacterium have the capacity to synthesize and release B vitamins.

Conclusion: A Symbiotic Nutritional Relationship

Microbes play a profoundly important and often underestimated role in our nutrition. From the exclusive synthesis of vitamin B12 by certain bacteria to the significant contribution of the gut microbiome to our supply of B-complex vitamins and vitamin K2, the microbial world acts as a hidden vitamin factory. While factors like diet and antibiotics can influence this delicate ecosystem, an optimized understanding of microbial vitamin production offers opportunities for improving human health, from dietary choices to the development of bio-enriched functional foods and probiotics. The symbiotic relationship between humans and their microbiota is a fascinating field with immense potential for redefining personalized health and nutritional strategies.

For a deeper dive into the metabolic pathways involved, explore this authoritative review: B Vitamins and Their Roles in Gut Health - PMC.

Frequently Asked Questions

Vitamin B12 is produced by specific bacteria and archaea, including species like Propionibacterium freudenreichii, Pseudomonas denitrificans, and some Lactobacillus species used in food fermentation. Within the human gut, Bacteroides fragilis and Fusobacterium varium are also known producers.

No, you cannot rely solely on your gut bacteria for all your vitamins. While the gut microbiome can produce a notable quantity of B and K vitamins, the amount and availability are not consistent or sufficient to meet daily requirements, and absorption can be limited.

Vitamin K1 (phylloquinone) is primarily synthesized by plants, especially leafy greens. Vitamin K2 (menaquinones) is mostly produced by bacteria, both in our gut and during food fermentation processes. While K1 is absorbed less efficiently, K2 from fermented sources is more bioavailable.

Antibiotics, particularly broad-spectrum types, can significantly disrupt the gut microbiome by killing off beneficial bacteria. This can lead to a decrease in the microbial synthesis of vitamins, potentially contributing to vitamin deficiencies.

Certain probiotic strains, particularly some Lactobacillus and Bifidobacterium species, are capable of synthesizing and releasing B vitamins. Some fermented foods containing these probiotics may increase vitamin levels, but their overall contribution to your total intake is not yet fully determined.

Diet has a profound effect on the gut microbiome's ability to produce vitamins. A varied diet, rich in fibrous foods, provides the necessary substrates for these microbes to thrive. For example, prebiotics can selectively stimulate the growth of beneficial bacteria, including some vitamin producers.

Industrial microbial fermentation is a highly efficient and cost-effective method for producing large quantities of vitamins for commercial use. It allows for the controlled, large-scale synthesis of vitamins like B2 and B12 for supplements, fortified foods, and animal feed, avoiding the high costs of chemical synthesis.