Everything you need to know about Cobalamin aka Vitamin B12 (v1.1)

Last updated: April 6th 2023

Table of Contents #

  1. Table of Contents
  2. Preface
  3. Stories
    1. The Cheese Cobalamin story
    2. The Steak Cobalamin story
    3. The Tuna Cobalamin story
    4. The Cobalamin and Folate story
    5. The Human Gut Cobalamin tragedy
  4. History
    1. The Discovery of Cobalamin
    2. On the name
  5. The Biosynthesis
    1. The B12 synthesizing bacteria
    2. Why plants are no home for our B12 synthesizers
    3. Intrinsic factor
    4. Life of an intrinsic factor
  6. Measuring Vitamin B12
    1. HPLC
    2. ELISA
  7. Processes
    1. P. freudenreichii makes Cobalamin
    2. Cobalamin goes from cheese to your body
    3. Food producer makes B12-rich cheese (general)
    4. Food producer makes B12-rich Emmental cheese
    5. Cobalamin makes dopamine and serotonin possible
  8. Economics
    1. Bacteria as input for food and supplement production
    2. Commercial suppliers of bacteria cultures
    3. Vitamin B12 supplement production process
    4. To be clear: All B12 comes from bacteria
    5. Purely synthetic B12: hard engineering and economics-wise
    6. Aquaculture
    7. Cobalamin production cannot be rushed
    8. For DIY hackers: Why retail milk sucks for making cheese
  9. Diet
    1. What a coincidence: A B12-rich diet is exactly ketocarnivore
    2. Eating multiple sources of B12
    3. Human B12 self-production: Too Little, Too Late
  10. Health
    1. Consequences of B12 deficiency
  11. Appendix
    1. The Human Gut
    2. Molecules have no conscience
    3. Bacterial metabolism
    4. Enzymes 101
    5. Free radicals. Chain reactions. Electrons.
    6. Why UV kills bacteria
    7. Acid Bacterium

Preface #

Let's kill all drivel, denial, and bullshit surrounding vitamin B12, for once and for all, shall we?

After you read this guide, you will understand literally everything you need to know about Cobalamin (aka Vitamin B12) forever.

Let's start with a few short (and silly) stories. They are my way to prepare you for the avalanche of autistic nerd talk that comes after.

Stories #

The Cheese Cobalamin story #

Once upon a time, in the kingdom of Camembert, where the cheese is said to be fit for royalty and the cows are known to have impeccable taste in grass, a humble cheese maker added a single P. freudenreichii bacterium to a vat of fresh milk. The bacterium wasted no time getting to work, devouring the lactose and other nutrients in the milk with great gusto, while producing lactic acid as a byproduct.

As the P. freudenreichii grew and multiplied, it began to produce a wondrous protein known as cobalamin, or Vitamin B12 to its friends. This bacterium was quite the artiste, using cobalt ions to craft this masterpiece of a vitamin, and the cheese maker had wisely added a sprinkle of cobalt to the milk to ensure there was enough for the P. freudenreichii to use.

For many hours, the P. freudenreichii continued to feast on the milk, producing both lactic acid and Vitamin B12. The cheese maker watched with great care, noting the pH of the milk as it dropped and the texture as it grew thicker and more curd-like.

At last, the cheese maker declared the fermentation complete, and it was time to separate the curds from the whey. With utmost delicacy, the curds were drained and pressed, then left to age for many weeks.

Over time, the P. freudenreichii continued its wondrous work, producing lactic acid and Vitamin B12, giving the cheese its distinctive flavor and texture. At last, the cheese was ready to be packaged and sold, and it became a beloved staple in the land's cuisine.

But as with all things in life, the P. freudenreichii's time in the cheese came to an end, and the Vitamin B12 and other nutrients it had produced were absorbed by those who consumed it, enriching their lives with essential nutrients and helping to support their health and well-being. And thus, the humble P. freudenreichii lived on, its legacy continued through the ages.

The Steak Cobalamin story #

In the dusty, windswept mountains of Argentina, where the gauchos (and hyperinflation) ride like the wind, the grill is always hot, and the cows are rumored to have an impeccable sense of style, there lived a curious little bacteria known as Propionibacterium freudenreichii. This fascinating microbiologists was well-known for its ability to produce vitamin B12, an essential nutrient for many animals, including, of course, humans - the most important animals of all.

One day, a bold and adventurous farmer decided to raise a cow in his field, where the grass grew tall and sweet. Little did he know that the P. freudenreichii bacteria were already there, lurking in the grass, waiting for their chance to make their mark.

As the cow grazed on the luscious grass, it ingested the bacteria, which then set to work in the cow's gut, producing vitamin B12 in abundance.

Years later, when the cow was slaughtered and its meat was cooked to medium rare perfection by a skilled chef, the vitamin B12 produced by the P. freudenreichii bacteria was still present, waiting to provide its essential nutrients to the human who consumed the steak.

Although it's unlikely that any significant amount of P. freudenreichii would be present in the center of a medium rare steak due to the high cooking temperature and searing process, the impact of the bacteria's work in the cow's gut cannot be denied. The vitamin B12 produced by these little organisms provides a crucial nutrient for the health and well-being of humans and other animals alike.

We shall always remember the hard-working P. freudenreichii bacteria that helped make it possible, and be grateful for the essential nutrients they provide.

The Tuna Cobalamin story #

In the briny depths of the ocean, there lived a merry band of bacteria, known as Pseudomonas denitrificans. These rascals roamed free, taking in all the nutrients they could find, until one day they stumbled upon a tuna fish.

In the tuna's gut, the Pseudomonas denitrificans met a group of veteran bacteria, called Propionibacterium freudenreichii, who had been living there since the tuna was a mere minnow. These wise bacteria had been quietly producing Vitamin B12 all along, as their own special brand of gut magic.

The Pseudomonas denitrificans quickly realized that there was a shortage of Vitamin B12 in the tuna's gut, and saw this as a chance to make themselves at home. They began to produce their own Vitamin B12 using the same metabolic pathways as the Propionibacterium freudenreichii, and slowly but surely, they gained dominance over the tuna's gut.

As the Pseudomonas denitrificans multiplied, the tuna started to produce more and more Vitamin B12, which was soon absorbed into its muscles and tissues. The day came when the tuna was caught by a fisherman and brought to the market, where it was purchased by a sushi chef.

As the chef sliced into the Vitamin B12-rich meat of the tuna, he knew that he had stumbled upon a treasure trove of essential nutrients. And so, thanks to the clever machinations of these oceanic bacteria, the people who consumed the sushi were able to maintain their health and vitality.

The Cobalamin and Folate story #

The city was dark and damp, and so was the lab where the two partners worked together. Agents Cobalamin (codename "B12") and Folate (codename "B9".) The dynamic duo, the Bonnie and Clyde of cell division.

Folate was the virtuoso designer, skillfully crafting DNA blueprints for new cells. But without Vitamin B12, her plans were nothing but empty promises. Vitamin B12 was the muscle, the enforcer who ensured that every blueprint was executed flawlessly. He was the one who ensured that the cells produced were healthy and functional.

It was a dangerous game, this "one-carbon metabolism." Folate and Vitamin B12 were a hard-boiled dynamic duo, working together to ensure the building blocks of life were just right.

Folate, also known as B9, was the brains of the operation. She knew just what to do to create the precursors to DNA and RNA molecules, making sure every new cell was perfect. But Folate knew she couldn't do it alone. She needed the muscle of B12 by her side. He was crucial for converting homocysteine, a harmful amino acid, into methionine, a necessary amino acid for protein synthesis.

Without B12, Folate could become trapped in an unusable form, leading to a buildup of homocysteine and an increased risk of health problems. It was a risky business, but with Folate's smarts and Vitamin B12's brawn, they made sure that "one-carbon metabolism" always ran smoothly.

But one day, Folate found herself in trouble. She had been taken in by a gang of free radicals, who were causing chaos in the city. These radicals weren't always bad - they were normally kept in check by antioxidants and the immune system, but something had gone wrong that day. The antioxidants were in short supply. The immune system was distracted by another problem. Folate was powerless to stop them on her own, and the fate of the entire operation hung in the balance. If the radicals continued to run rampant, they would destroy the very cells they were supposed to be protecting.

But Vitamin B12 had her back. He arrived just in time, wielding his powerful enzymes like a weapon. He neutralized the radicals and saved Folate from certain death.

Vitamin B12 was on a mission, and he wasn't going to let any radicals stand in his way. He knew that radicals were dangerous molecules that could damage important cellular components, like DNA and proteins. But Vitamin B12 had a trick up his sleeve - his powerful enzymes.

As he arrived on the scene, he could see the radicals wreaking havoc on the cell. They were stealing electrons from molecules left and right, causing a chain reaction of damage.

Vitamin B12 wasted no time. He quickly located the radicals and confronted them head-on. With his enzymes at the ready, he launched a counter-attack.

The battle was intense. The radicals were fierce and unrelenting, but Vitamin B12 was determined to emerge victorious. He used his enzymes to snatch up the stolen electrons from the radicals, effectively neutralizing them.

As the battle raged on, Vitamin B12 continued to wield his enzymes like a weapon. He was relentless in his pursuit of victory, and soon the radicals were on the ropes. They knew they were no match for the mighty Vitamin B12 and his powerful enzymes.

Finally, after what seemed like an eternity, the battle was won. The radicals were vanquished, and the cell was safe once again.

But Vitamin B12 knew that the fight against radicals was never truly over. He would need to stay vigilant, always ready to confront any threat to the cell's wellbeing. But with his powerful enzymes and unshakable determination, he was confident that he could take on anything that came his way.

From that day on, Folate knew that she could always count on Vitamin B12. Together, they would continue to produce the DNA necessary for cell division, fighting off any threat that came their way. They were the perfect partners in crime, and nothing could stop them.

The Human Gut Cobalamin tragedy #

Once upon a time, in a world that was both absurd and wonderful, there was a group of tiny but hardworking bacteria. They had one job: to make vitamin B12 for their human host.

These little bacteria worked tirelessly in the colon, churning out B12 by the bucketload. But no matter how much they made, it was never enough. Their host, a hapless human, was always deficient in B12.

The problem, you see, was that the colon is the very end of the digestive system. So, while these dedicated bacteria were busy making B12, the food that their host ate was already on its way out the other end.

Try as they might, the bacteria couldn't keep up. They begged and pleaded with their host to eat more B12-rich foods, but the human was stubborn and refused to change their ways.

In desperation, the bacteria even tried to build a pipeline, a direct route from the colon to the mouth. But the human was disgusted by the idea and refused to listen.

And so, the little B12-making bacteria continued to toil away in the colon, forever doomed to watch as their hard work was flushed away, never to benefit their host.

Moral of the story? Always eat your B12-rich foods, and don't take your dedicated little bacteria for granted. They're working hard for you, even if you can't always see it.

History #

The Discovery of Cobalamin #

Vitamin B12 was discovered in the 1940s by scientists who were studying pernicious anemia. It was identified as a "red-colored" compound that was essential for the growth of certain bacteria. Later, it was found to be a coenzyme, which means it helps enzymes in the body to carry out chemical reactions.

Vitamin B12 is synthesized only by certain microorganisms, and is not made by plants or animals.

On the name #

The word "Cobalamin" was coined by combining "Cobalt" with "vitamin" to describe the newly discovered vitamin that was found to contain Cobalt.

The "amin" part of "Cobalamin" refers to the chemical structure of the molecule. Specifically, Cobalamin is a type of molecule known as a "corrinoid", which has a ring structure that contains nitrogen atoms. The "amin" ending in "Cobalamin" comes from the fact that the nitrogen atoms in the ring are part of an amine group (-NH2).

So, in summary, "Cobalamin" is named after the element Cobalt, which is a key component of the molecule, and the "amin" ending, which refers to the nitrogen-containing ring structure of the molecule.

The Biosynthesis #

The B12 synthesizing bacteria #

Vitamin B12 is only synthesized by certain microorganisms. These microorganisms include bacteria, archaea, and some algae. They produce B12 through a process called biosynthesis, which involves a series of enzymatic reactions. (More on "enzymatic reactions" later.)

The quantities of B12 produced by these microorganisms vary depending on the specific species and their growth conditions. Some bacteria, such as Propionibacterium freudenreichii and Lactobacillus reuteri, are known to produce significant amounts of B12. There are various microorganisms known to produce Cobalamin, but for this guide our main Cobalamin-producing bacteria examples will be:

  1. Propionibacterium freudenreichii: First discovered by the French scientist Bernard-Jean-Baptiste Freudenreich in 1895. Freudenreich isolated the bacterium from Emmental cheese, which is a Swiss cheese known for its distinctive holes. The bacterium was initially called Bacillus freudenreichii, but it was later reclassified as Propionibacterium freudenreichii based on its biochemical and genetic characteristics. .

  2. Lactobacillus reuteri: First isolated from the feces of healthy pigs in 1980 by German microbiologists Gerhard Reuter and Michael Günther. The researchers were studying the microbial ecology of pig intestines and identified L. reuteri as a dominant bacterial species. The species was named after Reuter in recognition of his contribution to the field of microbiology.

  3. Pseudomonas denitrificans: It is a denitrifying bacterium, meaning it uses nitrate as a terminal electron acceptor instead of oxygen during respiration. Commonly found in aquatic environments, including marine and freshwater habitats. It is likely that Pseudomonas denitrificans was introduced into the ocean naturally, through the water cycle or via other organisms that live in water. Additionally, human activity such as shipping, oil drilling, and coastal development may also contribute to the spread of these bacteria in aquatic environments. Once in the ocean, Pseudomonas denitrificans can thrive on various sources of organic matter, including the remains of dead organisms, and can produce vitamin B12, which can then be consumed by other organisms in the food chain.

All these bacteria are known to produce significant amounts of vitamin B12.

During fermentation, P. freudenreichii and L. reuteri synthesize vitamin B12 and produce propionic acid. L. reuteri, a lactic acid bacterium, is capable of producing vitamin B12 and has been investigated for its potential health benefits, including gut health improvement and inflammation reduction. These bacteria are present in fermented foods, such as cheese and yogurt, and can be consumed as probiotic supplements. Similarly, Pseudomonas denitrificans is a gram-negative bacterium that is known for its denitrification ability, converting nitrate or nitrite into nitrogen gas. While Pseudomonas denitrificans is not known for its production of propionic acid or vitamin B12, it has been found to produce a range of other metabolites, such as pyocyanin, pyoverdine, and phenazines, that are involved in its interactions with the environment and other microbes.

Why plants are no home for our B12 synthesizers #

The reason P. freudenreichii and L. reuteri are found in animals and not plants is mainly due to their ability to thrive in the anaerobic conditions of animal digestive systems, as well as their ability to utilize the nutrients available in animal feed.

While plants also have a microbiome, the types of bacteria found in plant microbiomes are often different from those found in animal digestive systems. Additionally, the conditions in plant environments, such as exposure to sunlight and air, may not be suitable for the survival and growth of P. freudenreichii and L. reuteri.

Intrinsic factor #

Intrinsic factor is a glycoprotein that is produced by cells in the stomach lining called parietal cells. Its main function is to bind to vitamin B12 in the stomach and protect it from being degraded by stomach acid as it passes through the digestive tract.

It was first discovered in 1926 by a team of scientists led by William P. Murphy. They were studying pernicious anemia, a disease that causes fatigue, weakness, and other symptoms due to a lack of red blood cells. The team discovered that patients with pernicious anemia had a missing factor in their stomachs that was necessary for the absorption of vitamin B12.

In the years that followed, researchers identified this missing factor as intrinsic factor, a glycoprotein secreted by the parietal cells of the stomach. Intrinsic factor binds to vitamin B12 in the stomach and protects it from degradation by stomach acid, allowing it to be absorbed in the small intestine.

The term "intrinsic factor" was coined by the physician William P. Murphy and his colleagues in the 1950s to describe a substance they discovered in the stomach that was necessary for the absorption of vitamin B12. The name "intrinsic factor" was chosen because this substance was an inherent or intrinsic part of the gastric juice. In other words, it was not something that was added to the stomach from outside, but rather something that was produced within the stomach itself.

Since then, the term "intrinsic factor" has become synonymous with the protein that is required for the absorption of vitamin B12. The protein is synthesized by parietal cells in the stomach and binds to vitamin B12 in the small intestine, allowing it to be absorbed into the bloodstream. The name "intrinsic factor" has stuck, even though it does not provide any specific information about the vitamin B12 absorption pathway.

Since its discovery, researchers have made significant progress in understanding the role of intrinsic factor in the absorption of vitamin B12. However, there are still some unanswered questions, such as why some people have an autoimmune reaction that destroys the parietal cells and reduces intrinsic factor production.

In recent years, there has also been research on the potential role of intrinsic factor in other health conditions, such as neurological disorders and cancer. Overall, intrinsic factor remains a key area of study for researchers interested in understanding the complex chemistry of vitamin B12 absorption and utilization in the body.

Once intrinsic factor binds to B12, the complex travels to the small intestine, where it is absorbed by specific receptors in the terminal ileum, the last part of the small intestine. Without intrinsic factor, B12 would not be absorbed efficiently by the body, and deficiency could result.

Intrinsic factor production can be reduced or impaired in certain conditions, such as atrophic gastritis, which can lead to vitamin B12 deficiency even in people who consume adequate amounts of the vitamin.

Intrinsic factor is produced by the parietal cells of the stomach lining, so any condition or disease that affects these cells or the stomach lining can affect the production of intrinsic factor. One such condition is atrophic gastritis, which is a chronic inflammation of the stomach lining that can lead to a reduction in the number of parietal cells and intrinsic factor production.

Intrinsic factor deficiency can also be caused by certain autoimmune disorders, surgical removal of the stomach, and certain medications such as proton pump inhibitors and H2 blockers that reduce stomach acid production.

In cases where intrinsic factor deficiency is caused by a medical condition, treatment is focused on addressing the underlying cause. For example, in cases of atrophic gastritis, treatment may include medications to reduce inflammation, vitamin B12 supplements, and dietary changes.

Life of an intrinsic factor #

Once upon a time, in the depths of the stomach, a parietal cell was busy creating a special protein called intrinsic factor. This protein was destined to play a crucial role in the absorption of vitamin B12, an essential nutrient that the body needed to function properly.

After being synthesized, the intrinsic factor protein was secreted by the parietal cell and made its way to the small intestine, where it would encounter vitamin B12. When the intrinsic factor protein and vitamin B12 met, they formed a complex that allowed the vitamin to be absorbed into the bloodstream and transported to various parts of the body.

The intrinsic factor protein worked tirelessly to ensure that vitamin B12 was absorbed and utilized by the body. However, as time passed, the protein began to wear down and lose its functionality. Eventually, the intrinsic factor protein was broken down and eliminated from the body, but its legacy lived on.

Thanks to the hard work of the intrinsic factor protein, the body was able to maintain healthy levels of vitamin B12 and perform vital functions. Even though it was no longer present, the intrinsic factor protein's contributions were not forgotten and were essential to the overall health of the body.

Measuring Vitamin B12 #

To measure the production of vitamin B12, scientists begin by cultivating bacteria in a specially designed growth medium. Once the bacteria have been coaxed into producing the desired compound, researchers analyze the resulting culture to detect and quantify the amount of vitamin B12 present. This involves a range of cutting-edge techniques, including high-performance liquid chromatography (HPLC), enzyme-linked immunosorbent assay (ELISA), and various other microbiological assays.


HPLC, or high-performance liquid chromatography, was first developed in the late 1960s as an improvement on traditional liquid chromatography methods. It quickly gained popularity due to its ability to separate and identify individual compounds in complex mixtures with high precision and accuracy. Over the years, HPLC has undergone numerous technological advancements, including improvements in column materials, detectors, and data analysis software. Today, it is used in a wide range of industries, including pharmaceuticals, food and beverage, and environmental testing. The development of HPLC has revolutionized the field of analytical chemistry, allowing scientists to analyze and understand complex mixtures like never before.


ELISA, or Enzyme-Linked Immunosorbent Assay, was first developed in the 1970s as a way to detect and measure the presence of specific molecules, such as proteins or hormones, in biological samples. The technique involves coating a surface, such as a plastic plate, with a capture antibody that is specific to the target molecule. The sample is then added to the plate, and any target molecule in the sample will bind to the capture antibody.

Next, a detection antibody is added that is also specific to the target molecule, and that is conjugated to an enzyme that produces a colorimetric or fluorescent signal when it interacts with a substrate.

The plate is then washed to remove any unbound molecules, and the substrate is added. The enzyme-conjugated detection antibody will bind to any target molecule that is already bound to the capture antibody, and will catalyze the reaction of the substrate to produce a signal that can be detected and quantified.

Processes #

P. freudenreichii makes Cobalamin #

  1. P. freudenreichii takes up nutrients, including glucose and amino acids, from the cheese matrix and metabolizes them for energy and biosynthesis.
  2. As part of its metabolism, P. freudenreichii converts cobalt ions into the cobalamin precursor cobinamide.
  3. P. freudenreichii uses enzymes to convert cobinamide to cobalamin.
  4. Cobalamin is exported from P. freudenreichii into the cheese matrix, where it can be used by other organisms.

Note that other microorganisms in the cheese can also use the cobalamin produced by P. freudenreichii.

Cobalamin goes from cheese to your body #

  1. Cobalamin is synthesized by P. freudenreichii during cheese fermentation.
  2. Cobalamin is incorporated into the cheese matrix as it forms.
  3. During ripening, other microorganisms in the cheese can use the cobalamin for their own growth and metabolism.
  4. When the cheese is consumed by humans, the cobalamin can be released from the cheese matrix and is then available for absorption in the small intestine.
  5. Once absorbed, cobalamin binds to a transport protein called transcobalamin II, which delivers it to the liver for storage or to other cells for use in various metabolic processes.

Food producer makes B12-rich cheese (general) #

Here is a basic overview of the process involved in B12 production by P. freudenreichii in cheese:

  1. P. freudenreichii is added to the cheese during production.
  2. P. freudenreichii produces cobalamin (B12) during the fermentation process.
  3. The cobalamin produced by P. freudenreichii becomes bound to a protein called haptocorrin in the cheese.
  4. During digestion, haptocorrin releases the cobalamin into the small intestine.
  5. In the small intestine, the cobalamin binds to another protein called intrinsic factor.
  6. The cobalamin-intrinsic factor complex is absorbed into the bloodstream.
  7. The cobalamin is then transported to the liver, where it is stored and converted into the active forms of B12 (methylcobalamin and adenosylcobalamin).
  8. The active forms of B12 are then used in various cellular processes throughout the body.

Food producer makes B12-rich Emmental cheese #

Here's an expanded version of the B12 production process for Emmental cheese:

  1. Milk is pasteurized and inoculated with lactic acid bacteria, including P. freudenreichii.
  2. The mixture is incubated at a warm temperature to encourage bacterial growth and fermentation.
  3. Propionibacterium freudenreichii produces propionic acid, which reacts with the amino acid lysine to form the compound diacetyl.
  4. Diacetyl reacts with other compounds in the cheese to form acetoin and 2,3-butanedione.
  5. Propionic acid and CO2 gas produced by P. freudenreichii create pockets of air in the cheese, leading to the characteristic "eyes" or holes in Emmental cheese.
  6. Some strains of P. freudenreichii are able to produce B12 during the fermentation process, with the help of several enzymes involved in the biosynthesis of B12.
  7. The B12 produced by P. freudenreichii becomes incorporated into the cheese during the aging process, which can take several months.
  8. The cheese is typically aged for at least 4 months, during which time the bacteria continue to ferment and break down the cheese, developing its flavor and texture.

Cobalamin makes dopamine and serotonin possible #

OK, get ready for a turbocharged triple dose of nerd talk.

Let me give you an overview first, though, in case you don't wanna delve further:

Vitamin B12, also known as cobalamin, is a key player in many critical bodily functions. It is essential for the proper functioning of methionine synthase (MS), which is responsible for converting homocysteine to methionine. Without adequate levels of vitamin B12, this conversion cannot take place, leading to an accumulation of homocysteine in the body. Elevated homocysteine levels (due to lack of B12-produced homocysteine-to-methionine "converters," so to speak) are linked to various health problems, including cardiovascular disease, neurological disorders, and psychiatric conditions.

Now let's bring serotonin and dopamine into the picture. These neurotransmitters are synthesized from tryptophan, which requires methionine to be converted to S-adenosylmethionine (SAM), a critical cofactor in the conversion of tryptophan to serotonin and dopamine. Without sufficient methionine levels, the synthesis of these neurotransmitters is compromised, leading to mood disorders like depression and anxiety.

But that's not all. The conversion of L-DOPA to dopamine, another crucial neurotransmitter, also requires cobalamin-dependent enzymes. While the initial step of decarboxylating L-DOPA to dopamine does not require cobalamin, subsequent steps in dopamine synthesis do. For example, the conversion of dopamine to norepinephrine requires dopamine β-hydroxylase, which depends on vitamin C and cobalamin for proper function. Finally, the conversion of norepinephrine to epinephrine requires phenylethanolamine N-methyltransferase, which depends on SAM for its activity.

The cobalt ion at the center of the vitamin B12 structure is essential for its biological activity. This ion plays a critical role in the key reactions that vitamin B12 participates in, including the conversion of homocysteine to methionine and methylmalonyl-CoA to succinyl-CoA. Without this element at the core of vitamin B12, its ability to participate in these reactions would be altered.

(ASIDE: In general, the biological activity of vitamins is primarily influenced by their elemental structure. Different ions within the vitamin molecules impact their affinity towards certain molecules, ultimately determining their functionality.)

Finally, the moment you've been waiting for: the chemical breakdown. (Please try to contain your excitement.)

Methionine synthase (MS) is the enzyme responsible for converting homocysteine to methionine by transferring a methyl group from 5-methyltetrahydrofolate (5-MTHF) to homocysteine. MS requires a methylcobalamin coenzyme, which is formed by the binding of vitamin B12 to adenosylcobalamin. Homocysteine is first converted to methionine in a reaction that involves the transfer of a methyl group from 5-MTHF to cob(I)alamin, generating methylcobalamin. Methylcobalamin then transfers the methyl group to homocysteine, generating methionine and regenerating cob(I)alamin. The regenerated cob(I)alamin is converted back to the active coenzyme form of methylcobalamin in a reaction that requires the transfer of a methyl group from S-adenosylmethionine (SAM) to cob(I)alamin. Vitamin B12 plays a crucial role in this process by providing the necessary methylcobalamin coenzyme for MS to function properly. Without vitamin B12, MS cannot convert homocysteine to methionine, and the downstream effects on neurotransmitter synthesis and bodily functions can be severe.

Economics #

Bacteria as input for food and supplement production #

Starter cultures of P. freudenreichii and L. reuteri used for cheese production can come from a variety of sources. Some cheese makers may use naturally occurring bacteria present in the milk, while others may add specific strains of bacteria to the milk to achieve a desired flavor profile or texture. Additionally, starter cultures can also be obtained from commercial suppliers who specialize in producing bacteria cultures for use in cheese making.

Commercial suppliers of bacteria cultures #

Commercial suppliers often have a wide range of bacteria cultures available for purchase, including those that produce vitamin B12 and propionic acid. Some well-known suppliers in the industry include Chr. Hansen, Danisco, and DSM. These companies offer a variety of bacterial strains and mixtures to meet the specific needs of cheese makers, such as those that produce specific flavors or textures. By using commercial starter cultures, cheese makers can ensure consistency in their products and have access to a wider range of bacterial strains than may be available from natural sources.

Vitamin B12 supplement production process #

B12 supplements are made by using bacteria to synthesize the vitamin. The bacteria are grown in large fermentation tanks and then harvested, after which the B12 is extracted and purified. Some common bacteria used in the production of B12 supplements include Propionibacterium freudenreichii and Pseudomonas denitrificans.

The production of B12 by bacteria for supplement manufacturing usually occurs in a nutrient-rich medium. The specific medium used depends on the bacterial strain and the manufacturing process. The medium may contain ingredients like glucose, peptone, yeast extract, and mineral salts.

After the bacteria have synthesized the B12, the nutrient-rich medium is usually removed, and the B12 is purified through various methods. The B12 may be further processed into a dry powder or dissolved in a liquid before being used in supplements. It's possible that the B12 is eventually formulated into tablets or capsules for ease of use and consumption.

Other sources of B12 used in supplements can include animal products such as liver, eggs, and dairy, as well as fortified foods like breakfast cereals and nutritional yeast.

It is also possible to synthesize B12 in a lab, but this is not commonly done due to the high cost and complexity of the process.

To be clear: All B12 comes from bacteria #

All commercial sources of Vitamin B12, including supplements and fortified foods, are produced by bacterial fermentation or by using microbial cultures. Vitamin B12 is a complex organic molecule that can only be produced by certain bacteria, and it is not synthesized by plants or animals. Therefore, all dietary sources of Vitamin B12 ultimately come from bacterial sources.

While it is possible to produce cobalamin using recombinant DNA technology, the process still involves the use of bacteria to produce the protein that is then used to synthesize the vitamin. So in essence, bacteria are always involved at some point in the production of cobalamin.

Purely synthetic B12: hard engineering and economics-wise #

The synthesis of Vitamin B12 using purely synthetic methods is difficult for several reasons. First, the molecule is very complex, consisting of a large number of atoms arranged in a specific 3D structure. Second, the biosynthesis of B12 in nature involves a complex pathway of enzymes that are difficult to mimic in a laboratory setting.

While the inputs for B12 synthesis are commercially available, the challenge lies in putting these inputs together in the right way to form the complex B12 molecule. Synthetic chemists have been able to develop partial synthesis methods for B12, but these methods are often lengthy, costly, and require multiple steps. As a result, it is more economically feasible to obtain B12 from natural sources or through microbial fermentation, rather than through purely synthetic methods.

Aquaculture #

As we saw in the tuna story, the synthesis of B12 in tuna is an interesting case because it has a little plot twist: While tuna can produce small amounts of vitamin B12 in their own stomachs through Propionibacterium freudenreichii, the main source of vitamin B12 in tuna comes from the bacteria Pseudomonas denitrificans. These bacteria are found in seawater and are ingested by small fish, which are then eaten by larger fish, such as tuna. The Pseudomonas denitrificans in the gut of the tuna can then produce vitamin B12 from the cobalt present in the fish's diet.

This is, by the way, an example of one of the complications with fish farming: If tuna were farmed in tanks without access to Pseudomonas denitrificans, it is likely that the tuna would have lower levels of vitamin B12.

Aquaculture (fish farming) is a growing industry, and while there are some farms that raise tuna, most of the tuna sold in stores comes from the wild. However, as the demand for tuna continues to grow and overfishing becomes more of a concern, it is possible that more tuna will be farmed in the future. In that case, farmers may need to take measures to ensure that the tuna are receiving enough vitamin B12, either through their diet or by introducing the necessary bacteria into their tanks.

And it won't be as simple as just throwing the bacteria in the tanks, because the bacteria itself, ie, the Pseudomonas denitrificans, need to eat too, so it would haven to be a well-prepared content to be put in the tank.

The Pseudomonas denitrificans bacteria would need a source of nutrition in order to thrive and produce B12 in the tanks. It would be important to create a well-balanced ecosystem within the tank that would allow the bacteria to flourish and the tuna to thrive. This would likely involve developing a specialized feed that would provide the necessary nutrients for both the tuna and the bacteria. It could be a complex process, but if successful, it could potentially provide a sustainable source of high-quality, vitamin B12-rich tuna.

Cobalamin production cannot be rushed #

The rate of B12 production in cheese is dependent on the growth rate of the bacteria, which in turn is influenced by a variety of factors such as temperature, pH, and the availability of nutrients. Therefore, attempts to speed up the process too much may result in a lower yield of B12, or even inhibit the growth of the bacteria altogether. This is why traditional cheese-making methods often involve a slow, natural fermentation process that allows the bacteria to grow and produce B12 at their own pace.

For DIY hackers: Why retail milk sucks for making cheese #

The pasteurization process kills most of the microorganisms in milk, including P. freudenreichii and L. reuteri, that could be used for cheese production. Therefore, the milk you buy at the store does not contain these bacteria in significant amounts. To produce cheese, starter cultures containing these bacteria are usually added to the milk to initiate the fermentation process.

So, while it is possible to use pasteurized milk for cheese making, the process may not be as effective or efficient as using raw milk or specially treated milk, as certain components in milk that are important for cheese production may be lost or altered during pasteurization. Additionally, pasteurized milk is often homogenized, which can affect the texture and flavor of the resulting cheese.

Diet #

What a coincidence: A B12-rich diet is exactly ketocarnivore #

Here are some examples of natural whole foods and the respective bacteria involved in the production of vitamin B12:

Just look at the list of B12-rich foods.

Don't think I really need to say any more.

Eating multiple sources of B12 #

If you ate meat and cheese, both of them would likely have vitamin B12. They would not conflict with each other in the process of being absorbed by your body. In fact, consuming a variety of food sources of vitamin B12, including meat, fish, eggs, and dairy products, can help ensure adequate intake of this important nutrient.

The body absorbs vitamin B12 from food sources in the small intestine, where it is bound to intrinsic factor, a protein produced in the stomach. The intrinsic factor-vitamin B12 complex is then absorbed by the body's cells.

Human B12 self-production: Too Little, Too Late #


While it is true that some bacteria in the human gut produce vitamin B12, the amount produced is not sufficient to meet the body's needs, and it's not even produced at the right digestive stage. The bacteria that produce vitamin B12 in the gut are located in the colon, which is the final part of the digestive system.

Vitamin B12 is primarily absorbed in the small intestine, and the production of intrinsic factor by the stomach is necessary for its absorption. Therefore, even if some vitamin B12 is produced in the gut, it may not be effectively absorbed due to the lack of intrinsic factor production.

(See the appendix section on The Human Gut if you've forgotten the order of things.)

You would have to literally eat your own shit, so that your colon-produced vitamin B12 can pass through your stomach, where it can meet the intrinsic factor molecules it needs, to go into the small intestine where it will actually be absorbed into the bloodstream. Hey, maybe a hardcore enough vegan...

Seriously though, the vitamin B12 produced in your colon is just a byproduct of the natural process of bacterial fermentation. The colon is home to a diverse population of bacteria, which help to break down undigested food particles and produce various compounds, including short-chain fatty acids and gases like hydrogen and methane.

One of the byproducts of this fermentation process is vitamin B12. The bacteria that produce B12 in the colon are not specifically trying to make the vitamin for human use, but rather they are carrying out their own metabolic processes. They're just eating shit (literally?) and then themselves shitting out various outputs, including vitamin B12. And this happens to be taking place in the colon, not in the small intestines (where nutrients are absorbed into the bloodstream.)

Some animals, such as rabbits and horses, are able to extract significant amounts of vitamin B12 from their own colonic fermentation.

Bottom line is:

  1. The human digestive system is not designed to efficiently absorb vitamin B12 (or any nutrients in general) from the colon.
  2. The vitamin B12 that is produced there is not in a form that is usable by the body.
  3. Vitamin B12 is absorbed in the small intestine, not in the colon.
  4. (The colon is responsible for absorbing water and electrolytes and for storing feces until they can be eliminated from the body.)

Health #

Consequences of B12 deficiency #

From all we've seen, it shouldn't surprise you that B12 deficiency:

  1. Impairs DNA synthesis and cell division, because Vitamin B12 is required for the proper functioning of enzymes involved in these processes.
  2. Causes megaloblastic anemia, because Vitamin B12 is essential for the production of red blood cells, and a deficiency leads to the production of larger, immature red blood cells that cannot carry oxygen effectively.
  3. Increases the risk of cardiovascular disease, because a lack of Vitamin B12 can lead to an increase in homocysteine levels, which can damage the blood vessels and increase the risk of heart disease.
  4. Impairs neurological function, because Vitamin B12 is necessary for the proper functioning of the nervous system, including the brain and spinal cord.
  5. Causes nerve damage, because a deficiency of Vitamin B12 can lead to the destruction of the myelin sheath that surrounds and protects the nerves.
  6. Leads to fatigue and weakness, because the body cannot produce enough red blood cells to carry oxygen to the muscles and tissues.
  7. Causes memory loss and confusion, because Vitamin B12 is necessary for the proper functioning of the brain and nervous system.
  8. Affects mood and behavior, leading to depression and irritability, because Vitamin B12 plays a role in the synthesis of neurotransmitters that regulate mood and behavior.
  9. Causes a tingling or numbness in hands and feet, because the destruction of the myelin sheath can lead to nerve damage and abnormal sensations.
  10. Weakens the immune system, because Vitamin B12 is necessary for the proper functioning of white blood cells that fight off infection and disease.
  11. Increases the risk of bone fractures, because a deficiency of Vitamin B12 can lead to an increase in bone resorption and a decrease in bone density.
  12. Impairs fertility and fetal development in pregnant women, because Vitamin B12 is necessary for the proper development of the fetus and the production of healthy red blood cells in the mother.

Appendix #

The Human Gut #

  1. Mouth: The digestion process begins here with the mechanical breakdown of food by chewing and the chemical breakdown by enzymes in saliva.
  2. Esophagus: The esophagus is a muscular tube that connects the mouth to the stomach. It uses contractions to move the food down to the stomach.
  3. Stomach: The stomach mixes food with gastric juices, which contain hydrochloric acid and enzymes, to further break down the food into a liquid form.
  4. Small intestine: The small intestine is the longest part of the digestive system and is where most of the nutrients from food are absorbed into the bloodstream. It receives secretions from the pancreas and liver to help with digestion.
  5. Large intestine (colon): The colon absorbs water and electrolytes from undigested food, forming solid feces.
  6. Rectum: The rectum stores feces until they can be eliminated.
  7. Anus: The anus is the opening through which feces are eliminated from the body.

Molecules have no conscience #

In reality, molecules like vitamin B12 don't have a conscience or any cognitive ability to locate radicals. Rather, chemical reactions occur through a series of random molecular collisions. When B12 encounters a free radical, it's due to chance collisions between the molecules involved.

For instance, Vitamin B12 is not actively "seeking out" free radicals. Rather, it has an affinity for them due to the way its chemical structure is arranged. B12 contains a cobalt ion at its center, which makes it very reactive and able to easily donate or accept electrons. This chemical property allows B12 to participate in many reactions in the body, including the neutralization of free radicals.

When B12 comes into contact with a free radical, it's able to donate an electron to the radical, which neutralizes it and stops the chain reaction of damage. The enzyme systems that utilize B12 are able to regenerate the vitamin by adding another electron to it, so it can continue to neutralize free radicals.

The reason all these organic compounds do their jobs is akin to putting them all in a container, shanking the container, which makes them probabilistically (ie. in a way we personally cannot predict with full certainty) encounter each other and do what they need to do. Then we shake the container again, and any the new formations also meet each other randomly, and so on.

The study of how molecules interact with each other and their surroundings is known as molecular dynamics or computational chemistry. This field uses mathematical models and simulations to understand how molecules move and interact, and can provide insight into the behavior of complex chemical systems. Other related fields include chemical kinetics, which studies the rates of chemical reactions, and biophysics, which focuses on the physical principles that govern biological processes.

Bacterial metabolism #

Like all living organisms, P. freudenreichii and L. reuteri require a source of energy and nutrients to grow and produce vitamin B12.

P. freudenreichii is a propionic acid bacterium that can use a variety of substrates for growth, including lactate, ethanol, and glycerol. It is also capable of fermenting lactose and producing propionic acid as a major end-product.

L. reuteri is a lactic acid bacterium that is known to utilize carbohydrates such as glucose, fructose, and maltose as energy sources. It has also been shown to produce a variety of other metabolites, including lactic acid, acetic acid, and ethanol.

There are metabolic processes that occur when bacteria consume nutrients. The main outputs of this process are typically energy (in the form of ATP) and waste products (such as carbon dioxide and water). Organic acids are a byproduct that is produced alongside these other outputs.

The metabolic outputs of P. freudenreichii and L. reuteri can vary depending on the specific strain of the bacteria and the conditions in which they are grown. However, here are some of the known outputs of their metabolism:

  1. Vitamin B12: Both P. freudenreichii and L. reuteri are known to produce vitamin B12, which is an essential nutrient for humans.
  2. Organic acids: Both bacteria are acid-tolerant and produce a variety of organic acids as byproducts of their metabolism, including propionic acid, acetic acid, and lactic acid. These organic acids can contribute to the flavor and preservation of fermented foods.
  3. Exopolysaccharides: P. freudenreichii is known to produce exopolysaccharides, which are complex carbohydrates that can have prebiotic effects in the gut.

The measures of these metabolic outputs can vary depending on the specific output being measured. For example, vitamin B12 can be measured using microbiological assays or chromatographic methods, while organic acids can be measured using high-performance liquid chromatography (HPLC) or gas chromatography (GC). Exopolysaccharides can be quantified using methods such as the phenol-sulfuric acid assay.

Enzymes 101 #

In short: Enzymes are proteins that make things happen.

Enzymes are proteins that catalyze specific chemical reactions in the body or in other biological systems. They work by binding to specific molecules, called substrates, and converting them into different molecules, called products.

A complex pathway of enzymes refers to a series of enzymatic reactions that occur in a specific order to achieve a particular goal. Each enzyme in the pathway performs a specific function, and the products of one reaction become the substrates for the next reaction in the pathway. The efficiency and specificity of each enzyme in the pathway are critical for the overall success of the process.

The shape of a protein is what makes it act as an enzyme. Enzymes are typically globular proteins that have a specific three-dimensional structure or shape that is critical for their function. This shape is determined by the sequence of amino acids that make up the protein, and the way that the protein folds and interacts with itself and its surroundings.

The active site of an enzyme is a specific region on the surface of the protein that is responsible for binding to the substrate molecule and catalyzing the reaction. The shape and chemical properties of the active site are precisely tailored to fit the substrate molecule and facilitate the chemical reaction.

Therefore, the ability of a protein to act as an enzyme is dependent on its shape and the precise arrangement of its amino acid residues. Any changes to the protein's structure or sequence of amino acids can alter its function as an enzyme.

In the context of this guide: B12 itself does not carry enzymes. Instead, it is involved in the synthesis of enzymes that are needed for various biological processes. These enzymes are produced in the body and are then deployed to carry out their specific functions. B12 plays a critical role in the synthesis of these enzymes by providing a key component needed for their proper structure and function.

Free radicals. Chain reactions. Electrons. #

The chain reaction of damage occurs because free radicals are highly reactive molecules that can react with and damage other molecules in the body, causing them to become free radicals themselves. This can create a domino effect of damage that spreads throughout the body.

When B12's enzymes grab electrons from free radicals, they neutralize the radicals and convert them into stable molecules that are no longer harmful. The electrons that are grabbed become part of the enzymes and are used to stabilize them.

Enzymes themselves are not changed when they grab electrons from free radicals. Rather, they use the electrons to stabilize the free radicals and prevent them from causing further damage. In other words, the enzymes themselves remain intact, but the free radicals they neutralize are transformed into stable molecules.

Why UV kills bacteria #

UV radiation can damage bacteria, especially their DNA, as it can cause mutations and disrupt essential cellular processes. This is because bacteria do not have the protective mechanisms that eukaryotic cells have, such as a nuclear membrane and efficient DNA repair systems, to shield themselves from the damaging effects of UV radiation.

Some bacteria have developed certain mechanisms to cope with UV radiation, such as producing pigments that absorb UV radiation or forming biofilms that provide some protection. However, these mechanisms are not foolproof, and prolonged exposure to high levels of UV radiation can still be harmful to bacteria.

Acid Bacterium #

Both P. freudenreichii and L. reuteri are members of the acid bacterium group. Acid bacteria are a diverse group of bacteria that are characterized by their ability to produce large amounts of organic acids as byproducts of their metabolism. They are found in a wide variety of environments, including soil, water, and various food products.

In food, acid bacteria play an important role in the fermentation process, contributing to the unique flavor and texture of many fermented foods such as yogurt, cheese, sauerkraut, and pickles. Acid bacteria are also used in the production of various industrial products, such as citric acid, gluconic acid, and lactic acid.