One of the most interesting things about the good bacteria in our bodies is that they make the vitamins we need to survive. Forty to sixty percent of the human gut microbiome makes B vitamins, says a 2015 genomic study of 256 gut bacteria. Even better, gut bacteria make the active forms of some B vitamins such as tetrahydrofolate (folate) and P5P (vitamin B6), which the body can use quickly and easily.

We can’t make B vitamins by ourselves, yet we’ll die without them. It’s the same thing for other mammals. Even though B vitamins are common in food, they are destroyed easily during the cooking process. We don’t store them in our bodies, so we need a constant supply of B vitamins to stay healthy.

Photo by Jannes Jacobs on Unsplash

Enter our gut microbiota. We have coevolved with our friendly bacteria to get our nutritional needs met, especially in times of starvation or poor nutrition. And before you start thinking that bacteria are charitable, they also make B vitamins for their neighbors, who consume them.


A variety of bacteria under the microscope. Abstract vector created by macrovector –

Unlike vitamins from food, which are absorbed in the small intestine, vitamins produced by the gut microbiome are absorbed in the large intestine.1 Friendly gut bacteria take simple building blocks and manufacture complex vitamins, a process called de novo synthesis. Gut bacteria make these vitamins from scratch and they share them with us and with other bacteria in the microbiome.2

Without enough B vitamins, we feel tired, weak, anemic, our metabolism suffers, and we can’t detoxify our bodies. If we are low in folate, we can’t make red blood cells. We can’t turn on or off genes that are vital to health or disease. If we aren’t getting enough P5P, we can’t break down protein or make energy. Our mood suffers and we can’t think clearly. Without enough vitamin K, our bones become weak and brittle. We might develop calcium deposits in our arteries, blocking healthy blood flow.



Researchers have long known that gut microbiota make vitamins essential to human health, but little was known about precisely which bacteria produce which vitamins. Genomic research on the human microbiome is changing that.


Thiamin (Vitamin B1)

Thiamin is necessary for breaking down food and turning it into energy. It’s important for keeping a healthy weight, sharp memory, good mood, strong muscles, and a healthy heart.3


Bacteria in the Bacteroidetes and Fusobacteria phyla produce thiamin monophosphate. It’s also made to a lesser extent by Proteobacteria and Actinobacteria, but not by Firmicutes.2 Lactobacillus fermenti makes thiamin (3 ug/g of dry weight).2 Bacteroides fragilis, Bacteroides thetaiotamicron, Bacteroides vulgatus, Clostridium difficile, E. coli, Klebsiella pneumoniae, and Salmonella enterica subsp. enterica serovar Typhimurium all make thiamin.2


Thiamin levels were increased marginally by Streptococcus thermophilus ST5 and Lactobacillus helveticus R0052 during fermentation of a soy product. Lactobacillus helveticus and Bifidobacterium longum each increased thiamin slightly as well.4



Riboflavin (Vitamin B2)

Riboflavin is a cofactor in numerous chemical reactions in the body and participates in energy production.3 It is needed for a healthy throat, mouth, skin, and it prevents anemia.


Riboflavin is the second most commonly synthesized vitamin of the human gut microbiota.2 All Bacteroidetes and Fusobacteria have the genes to produce riboflavin.2 Ninety-two percent of Proteobacteria can synthesize riboflavin.2 Major bacterial producers of riboflavin are Bacillus subtilis and Escherichia coli.1 Other riboflavin producers are: B. fragilis, B. thetaiotaomicron, B. vulgatus, Clostridum difficile, Helicobacter pylori, K. pneumoniae, and Salmonella enterica subsp. enterica.2

Niacin (Vitamin B3)

Niacin participates in many chemical reactions throughout the body and is especially important in making energy, making fatty acids, and making hormones. It improves gut health, mood, energy levels, and memory.3


Niacin is the most commonly synthesized vitamin of the human gut microbiota. The majority of gut bacteria can make niacin, especially Bacteroidetes, Fusobacteria, and Proteobacteria. You may be able to get 27% of your niacin needs met by your good bacteria.2


Lactobacilli bacteria have been shown to make niacin and vitamin B6 in yogurt, cheese, and fermented products.1 B. fragilis, B. thetaiotaomicron, B. vulgatus, Clostridum difficile, E. coli, Helicobacter pylori, K. pneumoniae, Listeria monocytogenes, and Salmonella enterica subsp. enterica produce niacin.2 There are an estimated 1.12 million molecules of niacin in a single E. coli cell.2


Pyridoxine (Vitamin B6)

Vitamin B6 is critical for breaking down and metabolizing every bit of protein you eat. It’s an energy booster and improves mood and brain function since it promotes the production of neurotransmitters.


Human gut bacteria may contribute a whopping 86% of your daily vitamin B6 needs! The majority of Actinobacteria, Bacteroidetes, and Proteobacteria have the ability to synthesize pyridoxal 5’-phosphate, the active form of vitamin B6. Lactobacilli in fermented foods manufacture vitamin B6.1  B. fragilis, B. thetaiotaomicron, B. vulgatus, E. coli, K. pneumoniae, L. monocytogenes, and Salmonella enterica subsp. enterica produce vitamin B6.2



Pantothenic acid (Vitamin B5)

Pantothenic acid is a component of coenzyme A, which helps the body make fatty acids. Coenzyme A is essential for life. It helps to make energy from carbs, protein, and fats, folate derivatives, hormones,  vitamins A, D, and heme.5

Look to Bacteroidetes bacteria for making pantothenate.2 Several species of Proteobacteria and Actinobacteria also produce coenzyme A.6 B. fragilis, B. thetaiotaomicron, B. vulgatus, E. coli, Helicobacter pylori, K. pneumoniae, and Salmonella enterica subsp. enterica produce vitamin B5.2


Folate (Vitamin B9)

Folate is a hugely important vitamin. It is involved in a chemical process called methylation which provides the building blocks for making DNA, turning genes on or off, making good mood chemicals, and getting rid of toxins. Its critical role in human biochemistry explains why food was fortified with folate: because low levels can lead to birth defects,7 infertility, heart disease, and mood disorders.


Historically, Bifidobacteria species were believed to be the main folate producers in the gut microbiome. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis are high folate-producing species. Low folate-producing species are Bifidobacterium breve, Bifidobacterium longum subsp. longum, and Bifidobacterium adolescentis.1


However, recent genetic research shows that 13% of 512 human gut bacteria can make folate from scratch (or de novo synthesis).8 Lactobacillus reuteri and E. coli Nissle make folate (49-77 ng/uL). Akkermansia muciniphila, Clostridium sporogenes, and Prevotella copri also make folate.8 An additional 39% of the 512 human gut species can make folate as long as they have access to a precursor, pABA (para-aminobenzoic acid). Experts advise that L. reuteri should be given together with pABA to maximize its folate producing potential. Lactobacillus casei contains 22 uM of folate derivatives in each cell.2 Other folate producers are: B. fragilis, B. thetaiotaomicron, B. vulgatus, Clostridum difficile, E. coli, Helicobacter pylori, K. pneumoniae, Lactobacillus plantarum, L. monocytogenes, and Salmonella enterica subsp. enterica.2


Nearly all Bacteroidetes bacteria can produce folate.2 71% of Proteobacteria, 15% of Firmicutes, 26% of Actinobacteria, and 79% of Fusobacteria in the human gut are able to create folate de novo. From bacteria alone, you may be able to get 37% of your folate needs met. And remember, bacteria make the best form of folate- tetrahydrofolate- the active form that your body can use easily and quickly.8


“The microbiome serves as an important folate-generating ‘organ,’” authors said.8


Cobalamin (Vitamin B12)

Vitamin B12 is essential for cellular energy and DNA synthesis. It cooperates with folate in methylation and is similarly critical to optimum health. Vitamin B12 supports healthy pregnancies, positive mood, heart health, bone strength, and vision.9


Vitamin B12 stands out as the only vitamin that is made exclusively by bacteria. Neither animals, nor plants, nor fungi can make vitamin B12. All bacteria from the Fusobacteria phylum can make vitamin B12.2 Some experts suggest that 31% of your daily needs for vitamin B12 are manufactured by human gut bacteria.2


Propionibacterium freudenreichii, found in Swiss-type cheeses, was one of the first organisms known to biosynthesize vitamin B12. It is also used in the commercial production of vitamin B12.1 Lactobacillus reuteri CRL 1098 can make vitamin B12,1 to the tune of 50 ug/L vitamin B12 in each cell.2 Because Propionibacterium and Lactobacillus reuteri live in the human intestine, authors suggest that they may partially fulfill human vitamin B12 needs.1 Other gut bacteria that produce B12 are: B. thetaiotaomicron, Clostridum difficile, K. pneumoniae, L. monocytogenes, and Salmonella enterica subsp. enterica.2


Pseudomonas dentrificans, Rhodobacter capusulatus, Rhodobacter sphaeroides, and Sinorhizobium meliloti make cobalamin de novo. Salmonella typhimurium, Bacillus megaterium, Propionibacterium shermanii, and Escherichia coli make vitamin B12. Large scale industrial production of vitamin B12 uses Pseudomonas denitrificans, Propionibacterium shermanii, or Sinorhizobium meliloti. Thermotoga thermarum, Thermatoga lettingae, Fervidobacterium nodosum, and Thermosipho melanesiensis, Thermosipho africanus, Kosmotoga olearia, and Petrotoga mobilis also make cobalamin.10 Some or all of the bacteria in this paragraph and the one before it may not live in the human gut, as they were listed in a paper that also discussed commercial production of vitamin B12.


Vitamin K2 or Menaquinone


Vitamin K2 helps build durable, resilient bones for a lifetime. Good vitamin K2 levels make for a strong cardiovascular system because K2 promotes flexible and soft arteries that can pump blood smoothly.


Gut bacteria are believed to generate somewhere between 10 – 50% of your daily vitamin K needs. We still don’t know a lot about the vitamin K2 producers in the human microbiome.11 However, we do know that Escherichia coli, Mycobacterium phlei, and Bacillus subtilis make menaquinones, as they were the subject of extensive research.12 As of a 1995 publication, few human commensal microbes were believed to be major producers of vitamin K2. However, other research says the obligate anaerobes in the Bacteroides fragilis, Eubacterium, Propionibacterium, and Arachnia groups are menaquinone producers. Bacillus brevis and Bacillus cereus make menaquinone. Bacillus natto is responsible for high levels of MK-7 in the soybean fermentation product, natto.13



Biotin is a key cofactor in breaking down fats, carbs, and protein to make energy. Biotin supports healthy hair, nails, and skin. It helps control blood sugar.


Approximately 40% of the gut microbiome can make biotin. The majority of Bacteroidetes, Fusobacteria, and Proteobacteria genomes have what they need to synthesize biotin de novo.2 B. fragilis, B. thetaiotaomicron, B. vulgatus, E. coli, Helicobacter pylori, K. pneumoniae, L. plantarum, and Salmonella enterica subsp. enterica produce biotin. E. coli cells contain 40 uM biotin.2

Other bacteria that make biotin include:14

  • Bacillus sphaericus
  • Bacillus subtilis
  • Brevibacterium flavum/Cornebacterium glutamicum
  • Kurthia spp.
  • Mesorhizobium loti
  • Methylobacillus flagellatum
  • Sinorhizobium meliloti


The Biosynthesis of “B Complex” by Gut Bacteria

Some human gut bacteria make not only one B vitamin but a “B complex.” Bacteria from the Bifidobacteriaceae family are more likely to make niacin, vitamin B6, and thiamin. Of the Bacteroidetes phylum, 51% were able to produce all eight B vitamins. Several Proteobacteria can also make all eight B vitamins. Conversely, bacteria from the Firmicutes phylum were not able to biosynthesize any B vitamins!2 It’s interesting that a high Firmicutes to Bacteroidetes ratio has been linked to metabolic syndrome and obesity.15 Higher Bacteroidetes phylum may not only indicate a healthier microbiome, a leaner body, but also higher levels of vitamin production.


We Still Need Vitamins from Food and Supplements

Even though healthy gut bacteria contribute to vitamin levels, we cannot rely on them to meet all of our vitamin needs. A major reason we can’t count on them is because the rest of the microbiome uses these vitamins, too. Based on calculations, your good gut bacteria make only four vitamins in sufficient amounts to supply at least ¼ of your daily B vitamin needs – vitamin B12, folate, niacin, and vitamin B6.2 That means you still need to eat a healthy diet and take your vitamins. But if you take antibiotics, you will need to boost your diet and supplements because your microbiota-derived vitamins will take a nosedive.


Action Steps: Boost Your Nutrition by Maximizing Your Gut Microbiome

  • Foster a healthy microbiome with a whole foods diet including dietary fiber and plenty of plant foods.
  • Rebuild your microbiome with probiotics and prebiotics.
  • Avoid unnecessary antibiotics.
  • Eat fermented foods such as coconut kefir or fermented vegetables, which may be high in vitamins due to bacterial biosynthesis.
  • Take a daily, high-quality multivitamin-mineral supplement and B complex.
  • If you must take antibiotics, be sure to boost your vitamin supplementation, as your vitamins will likely take a hit.
  • Check stool test results (such as the GI-MAP) for healthy levels of these vitamin-producing microbes:
    • Bacteroides fragilis
    • Bifidobacteria species
    • Lactobacillus species
    • Escherichia coli
    • Akkermansia muciniphila
    • Bacillus species
    • Bacteroidetes phylum
    • Firmicutes phylum
    • Fusobacteria phylum




  1. LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol. 2013;24(2):160-168.
  2. Magnusdottir S, Ravcheev D, de Crecy-Lagard V, Thiele I. Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Frontiers in genetics. 2015;6:148.
  3. I.O.M. Dietary reference intakes for thiamin, riboflavin, niacin, vitamin B6, folate, vitamin B12, pantothenic acid, biotin, and choline. Washington D.C.: National Academy Press; 2000:1-592.
  4. Champagne CP, Tompkins TA, Buckley ND, Green-Johnson JM. Effect of fermentation by pure and mixed cultures of Streptococcus thermophilus and Lactobacillus helveticus on isoflavone and B-vitamin content of a fermented soy beverage. Food Microbiol. 2010;27(7):968-972.
  5. Higdon J. Pantothenic acid. Micronutrient Information Center 2004. Accessed August 31 2015.
  6. Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol. 2016;7:1144.
  7. Scholl TO, Johnson WG. Folic acid: influence on the outcome of pregnancy. Am J Clin Nutr. 2000;71(5 Suppl):1295S-1303S.
  8. Engevik MA, Morra CN, Roth D, et al. Microbial Metabolic Capacity for Intestinal Folate Production and Modulation of Host Folate Receptors. Front Microbiol. 2019;10:2305.
  9. O’Leary F, Samman S. Vitamin B12 in health and disease. Nutrients. 2010;2(3):299-316.
  10. Fang H, Kang J, Zhang D. Microbial production of vitamin B12: a review and future perspectives. Microb Cell Fact. 2017;16(1):15.
  11. Walther B, Karl JP, Booth SL, Boyaval P. Menaquinones, bacteria, and the food supply: the relevance of dairy and fermented food products to vitamin K requirements. Adv Nutr. 2013;4(4):463-473.
  12. Bentley R, Meganathan R. Biosynthesis of vitamin K (menaquinone) in bacteria. Microbiol Rev. 1982;46(3):241-280.
  13. Suttie JW. The importance of menaquinones in human nutrition. Annu Rev Nutr. 1995;15:399-417.
  14. Streit WR, Entcheva P. Biotin in microbes, the genes involved in its biosynthesis, its biochemical role and perspectives for biotechnological production. Appl Microbiol Biotechnol. 2003;61(1):21-31.
  15. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444(7122):1027-1031.

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, MS, is a researcher, author, educator, and laboratory consultant. She studied medicinal plants in the rain forests of Panama as a Fulbright Scholar and then launched a career in science and natural medicine. Early on, she studied ethnobotany, ethnopharmacology, and drug discovery at the University of Georgia and AptoTec, Inc. She joined innovators at Metametrix Clinical Laboratory as a medical education consultant helping clinicians use integrative and functional laboratory results in clinical practice. She owns Health First Consulting, LLC, a medical communications company with the mission to improve human health using the written word. Ms. Nelson-Dooley is an oral microbiome expert and author of Heal Your Oral Microbiome. She was a contributing author in Laboratory Evaluations for Integrative and Functional Medicine and Case Studies in Integrative and Functional Medicine. She has published case studies, book chapters, and journal articles about the oral microbiome, natural medicine, nutrition, laboratory testing, obesity, and osteoporosis.