Vitamin-Producing Microbes

Vitamin-Producing Microbes

Micronutrient deficiency is a common problem, especially for people following a standard american diet (SAD), but even among those of us who follow an ancestral diet. Even when eating whole, nutrient-dense foods and avoiding processed, nutrient-robbing foods, it can be challenging to get everything our bodies need. Fortunately, it seems that our gut bacteria may help to fill in some of the gaps.

In this post, I’m going to talk about B vitamins, as there is a huge chunk of research focused on the topic. There is evidence that bacteria can supply other vitamins as well, and I?m planning to address those other nutrients in a future post. B-vitamin deficiency is a common symptom of small intestinal bacterial overgrowth (SIBO), indicating that a healthy gut with sufficient ratios of ‘good’ bacteria is necessary for proper nutrient production and absorption. Gut bacteria are able to synthesize/produce most B vitamins, such as folate, biotin, B12, thiamine, and niacin. Bifidobacterium sp. in particular seem to be good at synthesizing vitamins, with some strains being much better producers than others. Importantly, the synthesized vitamins aren’t just hanging out in the gut once they’re made. There are systems within the large intestine that allow our bodies to absorb and utilize these bacterially-produced vitamins.

Individual B Vitamins

B vitamins are often found together in foods and are all important for cell metabolism. However, each individual vitamin is distinct and has a unique function in the body. Folate can’t replace biotin, etc. They are also frequently produced by some of the same bacterial strains, with some differences depending on the individual vitamin. In some cases, B vitamin production is a bit of an insurance policy for our bodies. In case we don’t get enough of the nutrients in our food, our gut microbes can pick up the slack until we find another source. Here, I address some of the most commonly discussed and vital members of the B-group vitamins.

Folate is essential for numerous functions such as vitamin, nucleotide, and amino acid synthesis and DNA replication, repair, and methylation. Folate is especially important during pregnancy, as it is critical for fetal development and the prevention of neural tube defects. Certain strains of bifidobacteria species have been shown to produce folate. Bifidobacterium bifidum (B. bifidum) and Bifidobacterium infantis (B. infantis) appear to be the strongest producers of folate, and both humans and rats have increased production of the nutrient when fed these strains. Note that folate is different from folic acid, a synthetic nutrient that is prevalent in prenatal vitamins. If you are pregnant or considering becoming pregnant, make sure to look for a supplement with folate and not folic acid. My favorite is Seeking Health Optimal Prenatal.

Biotin is important for cell growth and for the metabolism of fat, protein, and carbohydrates. Evidence suggests that biotin is absorbed from both dietary and bacterial sources. Researchers have found that fecal concentrations of biotin are higher than what would be expected based on intake from food. This suggests that something is happening with the gut flora to produce the B vitamin. Bifidobacterium species are effective producers of biotin, with B. bifidum producing the most biotin. This may provide us with an important non-food source of biotin.

Vitamin B12 was first discovered when researchers found that liver could be used to treat pernicious anemia (now also called B12 anemia). B12 was identified as the compound in liver that cured the illness. B12 is exclusively produced by microorganisms. Meaning that animals are not capable of making our own. However, it can be found in other foods (such as liver) due to bacterial symbiosis. The vitamin is important for nervous system and brain function, and deficiency is associated with increased risk for heart attack, stroke, and vascular disease. New research suggests that deficiency may also be linked to several neurological and psychiatric symptoms. Numerous microbe species produce B12, including Aerobacter, Agrobacterium, Bacillus, Lactobacillus, Propionibacterium, and Pseudomonas, some of which may partially fulfill our B12 requirement.

[Side note: The fact that humans and other animals require B12 for survival but are incapable of producing it is another reminder of how tightly linked we are with microbes.]

Thiamine, or vitamin B1, is important for neurological health. It is used by our bodies in the production of the neurotransmitters acetylcholine and GABA, both of which are critical for function of the central and peripheral nervous systems. These neurotransmitters affect the entire body, from brain to heart to skeletal muscles and beyond. Only bacteria, fungi, and plants have been shown to produce thiamine, so as animals, we need to obtain it from our diet and support the gut bacteria that produce it. B. bifidum and B. infantis are capable of producing relatively large quantities of thiamine. Both of these occur naturally in the human gut, and it is possible to increase their quantities through diet and lifestyle.

Niacin, or vitamin B3/nicotinic acid, is an essential nutrient, whose importance is often characterized by the consequences of insufficient intake. Symptoms such as nausea, skin problems, headaches, and, in severe cases, pellagra can result from niacin deficiency. Niacin has also been researched for its LDL cholesterol-lowering and HDL-raising capabilities. Similar to other B vitamins, B. bifidum and B. infantis appear to be good producers of niacin.

Grow Your Own Bifidobacteria

Now that we know Bifidobacterium, and especially B. bifidum and B. infantis appear to be the superbugs of B-vitamin production, what do we do about it? In order to produce vitamins in the gut, we need to have the bacteria that do the synthesizing. There are a number of ways to increase composition of bifidobacteria through food. One is to eat foods with oligosaccharides. Some examples are honey, tapioca, kimchi, garlic, and asparagus. Polyphenol-rich foods like those I talked about last week may be helpful as well.


It can also be beneficial to ‘re-stock’ our Bifidobacterium stores with a high quality probiotic. Including a good probiotic can be very helpful, especially following?a course of antibiotics. These are the options I recommend most highly:

ProBioita HistaminX – This is the probiotic I use and I am extremely happy with it. It has a good variety of strains and is formulated to prevent excess histamine release, which is something I struggle with.

Bio-Kult – Another great option, Bio-Kult is a broad-spectrum formula containing 14 strains of bacteria. This product is frequently recommended to those on the GAPS diet.

For more in-depth information?about the ways we can increase the good bacteria in our guts, check out this post on bolstering bifidobacteria.

For now, here’s a cute puppy picture:

Newton likes to make dirt beds. And probably ingests lots of soil-based microbes in the process :)
Newton likes to make dirt beds. And probably ingests lots of soil-based microbes in the process 🙂


Deguchi et al. (1985). Comparative studies on synthesis of water-soluble vitamins among human species of bifidobacteria. Agricultural and Biological Chemistry, 48, 13-19.

Hill, M. (1997). Intestinal flora and endogenous vitamin synthesis. European Journal of Cancer Prevention, 6(2), 143-145.

LeBlanc et al. (2013). Bacteria as vitamin suppliers to their host: A gut microbiota perspective. Current Opinion in Biotechnology, 24(2), 160-168.

Martens et al. (2002). Microbial production of vitamin B12. Applied Microbiology & Biotechnology, 58(3), 275-285.

Noda et al. (1994). Biotin production by bifidobacteria. Journal of Nutritional science and Vitaminology, 40(2), 181-188.

Said & Mohammed. (2006). Intestinal absorption of water-soluble vitamins: An update. Current Opinion in Gastroenterology, 22(2), 140-146.

Yen et al. (2011). Beneficial effects of fructo-oligosaccharides supplementation on fecal bifidobacteria and index of peroxidation status in constipated nursing-home residents – A placebo-controlled, diet-controlled trial. Nutrition, 27(3), 323-328.

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