Handbook - Metabolites

Vitamins

The gut microbiome regulates vitamin levels by synthesizing essential vitamins like B and K, enhancing nutrient absorption, and supporting gut barrier integrity. Beneficial microbes influence metabolism and immune responses, optimizing vitamin utilization. A balanced, fiber-rich diet and fermented foods help maintain microbial diversity for effective vitamin regulation and overall health.

Vitamin A

The gut microbiome plays a vital role in vitamin A metabolism by influencing its absorption, conversion, and storage. Certain gut bacteria, such as Bacteroides and Firmicutes, help break down dietary components that enhance the bioavailability of vitamin A and its precursors, like beta-carotene. Some microbes can also regulate the expression of host enzymes involved in converting carotenoids into retinol (active vitamin A). Additionally, the gut microbiota impacts the immune response and gut barrier integrity, both of which are crucial for proper vitamin A utilization.

To maintain a healthy gut microbiome that supports vitamin A metabolism, a diet rich in fiber, prebiotics, and diverse plant-based foods is essential. Fermented foods like yogurt, kefir, and kimchi, as well as probiotics, can promote beneficial bacteria. Avoiding excessive antibiotics, managing stress, and staying physically active also support microbial balance. A diverse, nutrient-rich diet is key to supporting both gut and vitamin A health.

Vitamin B

The gut microbiome plays a crucial role in regulating B vitamin availability, including B1 (thiamine), B2 (riboflavin), B3 (niacin), B5 (pantothenic acid), B6 (pyridoxine), B7 (biotin), B9 (folate), and B12 (cobalamin). Various gut bacteria—such as Bifidobacterium, Lactobacillus, Enterococcus, and Escherichia coli—synthesize B vitamins or enhance their bioavailability. These vitamins are vital for energy production, DNA synthesis, nerve function, and immune health. The gut microbiota also helps regulate host absorption and maintains a balanced supply, preventing deficiencies or excesses that could disrupt cellular functions.

To support gut microbiome balance and optimal B vitamin regulation, consume a diverse, fiber-rich diet with whole grains, leafy greens, legumes, and fermented foods like yogurt or kimchi. Prebiotics (e.g., in onions, garlic, and bananas) nourish beneficial bacteria. Avoid overuse of antibiotics, reduce stress, and stay physically active to maintain microbial diversity. These habits foster a healthy gut environment that promotes efficient B vitamin regulation and overall well-being.

Vitamin C

The gut microbiome plays an indirect but important role in vitamin C regulation by supporting gut health, reducing oxidative stress, and enhancing nutrient absorption. While most gut bacteria do not produce vitamin C, families like Lachnospiraceae contribute by maintaining gut barrier integrity and producing short-chain fatty acids (SCFAs), which reduce inflammation and promote efficient absorption of nutrients, including vitamin C. A balanced gut microbiome also helps modulate immune responses, complementing vitamin C’s antioxidant and immune-boosting effects.

To maintain microbial balance, especially Lachnospiraceae, consume a fiber-rich diet with fruits, vegetables, whole grains, and prebiotics. Include fermented foods like yogurt or kimchi to support diversity. Avoid excessive antibiotics and processed foods, and manage stress levels. These practices promote a healthy gut environment that supports optimal vitamin C utilization and overall health.

Vitamin D

The gut microbiome plays a key role in vitamin D regulation by influencing its metabolism, absorption, and immune-modulating effects. While vitamin D is primarily synthesized in the skin, gut bacteria help optimize its activation and function. Species like Coprococcus catus and Blautia obeum support gut barrier integrity and reduce inflammation, creating favorable conditions for vitamin D absorption. Coprococcus catus also produces short-chain fatty acids that enhance immune balance, while Blautia obeum is linked to healthy vitamin D metabolism and improved host immune response.

To maintain microbial balance and support vitamin D regulation, consume a fiber-rich diet including whole grains, fruits, and vegetables, along with fermented foods to nourish beneficial microbes. Limit processed foods, manage stress, and avoid overuse of antibiotics. Adequate sun exposure and dietary sources of vitamin D also complement a healthy microbiome for optimal vitamin D function and overall well-being.

Vitamin K

The gut microbiome plays a direct role in vitamin K regulation, particularly in producing vitamin K2 (menaquinone), which is essential for blood clotting, bone health, and cardiovascular function. Certain gut bacteria—especially Bacteroides, Escherichia coli, and members of the Firmicutes phylum—synthesize vitamin K2 in the colon, contributing to the host’s overall vitamin K levels. Though much of this is produced in the large intestine where absorption is limited, it still supports systemic health over time.

To maintain a gut microbiome that supports vitamin K regulation, eat a balanced diet rich in leafy greens (vitamin K1) and fermented foods like natto, yogurt, and kefir (vitamin K2). Fiber from fruits, vegetables, and whole grains supports beneficial bacteria. Avoid unnecessary antibiotics, manage stress, and stay active to maintain microbial diversity and gut health, promoting effective vitamin K metabolism and absorption.

Short Chain Fatty Acids

The gut microbiome regulates short-chain fatty acids (SCFAs) by fermenting dietary fibers, producing SCFAs like acetate, propionate, and butyrate. These SCFAs support gut health, reduce inflammation, and improve immune function. A diet rich in fiber, prebiotics, and fermented foods helps maintain microbial diversity and optimal SCFA production for health benefits.

Acetate

The gut microbiome regulates acetate levels through fermentation of dietary fibers, with acetate serving important roles in gut barrier integrity, immune modulation, and lipid metabolism. Key microbes involved in acetate production include Akkermansia muciniphila, Blautia hydrogenotrophica, and Ruminococcus bromii. A. muciniphila degrades mucins and supports gut lining health, indirectly enhancing acetate production. B. hydrogenotrophica contributes to acetate generation by consuming hydrogen, balancing microbial fermentation. R. bromii specializes in breaking down resistant starch, releasing substrates that promote acetate and other short-chain fatty acid production.

To maintain a balanced microbiome for healthy acetate regulation, consume a fiber-rich diet with whole grains, legumes, fruits, and vegetables. Include prebiotics and fermented foods to support microbial diversity. Avoid excessive use of antibiotics and processed foods, and manage stress. These habits promote the growth of beneficial microbes, ensuring steady acetate production and overall gut and metabolic health.

Butyrate

The gut microbiome regulates butyrate levels by fermenting dietary fibers, with butyrate playing a key role in maintaining colon health, reducing inflammation, and supporting immune function. Key butyrate-producing bacteria include Faecalibacterium prausnitzii, Roseburia, Eubacterium, and Butyricicoccus. Butyrate serves as the main energy source for colonocytes and helps strengthen the gut barrier.

To support butyrate production, consume a diet rich in soluble fiber and resistant starch from foods like oats, legumes, bananas, and vegetables. Fermented foods and prebiotics also nourish beneficial microbes. Avoid excessive antibiotics and processed foods to preserve microbial diversity. These practices enhance the abundance of butyrate-producing bacteria for optimal gut and overall health.

Propionate

The gut microbiome regulates propionate levels through fermentation of dietary fibers, particularly by bacteria such as Bacteroides, Veillonella, and Akkermansia muciniphila. Propionate plays important roles in glucose metabolism, appetite regulation, and anti-inflammatory responses. It also supports liver function and helps maintain gut barrier integrity.

To promote healthy propionate production, consume a diet high in fermentable fibers and resistant starches from sources like legumes, oats, apples, and root vegetables. Including prebiotics and fermented foods helps support beneficial microbes. Avoiding processed foods, unnecessary antibiotics, and managing stress are essential for maintaining microbial balance and diversity, ensuring effective and consistent propionate production for metabolic and gut health.