What is the Most Effective Way to Boost Bifidobacteria?

April 17, 2022 6 min read

What is the Most Effective Way to Boost Bifidobacteria? - Layer Origin Nutrition

What is the Most Effective Way to Boost Bifidobacteria?

The gut microbiome constitutes a vast and diverse ecosystem of viruses, bacteria, and fungi.  With respect to bacteria, there are upwards of 100 trillion present in the gut ranging more than 5,000 species. Among these are a genus of bacteria known as Bifidobacteria, the first habitant in your gut when you were an infant.

 What are Bifidobacteria?

Bifidobacteria are obligate anaerobes (i.e., bacteria that can only grow in low-oxygen conditions) that live in the colon.

They are responsible for breaking down key indigestible carbohydrates into small molecules that feed other key species of bacteria in the gut. Supporting Bifidobacterial growth is a key strategy to increase overall microbial diversity in the gut, which is an important characteristic of a healthy microbiome.

The process by which metabolic products made by one species of bacteria are consumed by other species of bacteria is known as a cross-feeding interaction. Notably, the cross-feeding interactions supported by Bifidobacteria are especially effective at boosting the butyrate-producing bacteria in the gut.

Bifidobacteria is often referred as the foundation bacteria in the gut ecosystem.

What short chain fatty acid do Bifidobacteria produce?

Short chain fatty acids (SCFAs), like butyrate, are the product of the fermentation of fiber and other indigestible carbohydrates by specific species of anaerobic bacteria in the colon. The most abundantly produced SCFAs are acetate, propionate, and butyrate which are present in a roughly 3:1:1 ratio in a healthy colon.

While bacteria within the phylum Firmicutes are the primary butyrate producers (e.g., Faecalibacterium prausnitzii and Clostridium leptum), Actinobacteria like Bifidobacteria produce acetate and lactate which can subsequently feed bacteria in phylum Firmicutesand thereby promote butyrate production.

What is Butyrate?

Not only is butyrate the primary fuel source for colonocytes (colon cells), but it is also involved in the maintenance of the gut barrier by supporting the integrity of tight junctions (i.e., the connections between cells in the intestines). The breakdown of these tight junctions leads to a phenomenon known as leaky gut where bacterial endotoxin enters into the circulation and drives systemic inflammation in the body.

Not only does butyrate exert anti-inflammatory actions by preventing and ameliorating leaky gut, but it also directly inhibits inflammatory signaling pathways and stimulates the release of anti-inflammatory cytokines by immune cells.

Butyrate also modulates gene expression and regulates cellular proliferation which results in anti-cancer effects in the colon.

How Bifidobacteria Can Help to Prevent Certain Diseases

Strikingly, breast-fed infants have a gut microbiome composed of up to 60-90% Bifidobacteria thanks to the unique oligosaccharide profile of breast milk. High levels of Bifidobacteria in the infant gut are critical for the development of a healthy immune system.

Babies with depleted Bifidobacteria populations due to exposures like antibiotics or formula feeding are at a significantly higher risk of developing an autoimmune condition later in life.

Bifidobacteria also plays an important role in the adult gut. Declines in populations of Bifidobacteria in the gut occur in response to aging and are associated with the development of age-related diseases, most of which arise from low-grade inflammation sustained over decades (i.e., "inflamm-aging").

The anti-inflammatory activities that Bifidobacteria exert via cross-feeding interactions and immune modulation help to mitigate this low-level inflammation and support a healthy aging process.

Moreover, the implementation of dietary and supplementation strategies to optimize for the growth of Bifidobacteria, and thereby butyrate production, may reduce or prevent leaky gut, inflammatory bowel disease (IBD), ulcerative colitis, and bowel cancers.

Bifidobacteria also synthesize B vitamins, which are critical cofactors for energy metabolism, and prevent the colonization of pathogenic strains of bacteria in the gut.

Dietary Approaches to Supporting Bifidobacteria Populations

Prebiotics are molecules that pass through the digestive system intact and reach the colon where they can feed the microbiome. Consumption of prebiotics such as polyphenols, soluble fibers, resistant starches, GOS, FOS, and HMOs like 2’-fucosyllactose directly feed Bifidobacteria and support their growth.

  • Premium Prebiotics: 

GOS, FOS, and HMOs have been used in infant formula to boost the bifidobacteria in the infant’s gut. They are clinically proven prebiotics and very effective in boosting bifidobacteria in the gut.
  • Foods containing Polyphenols: 

Apple peels, black and green tea, dark chocolate, coffee, olives, olive oil, turmeric, and dark fruits like pomegranate, cranberries, blueberries, blackberries, and raspberries.
    • Foods containing Soluble Fibers:

    Apples, pears, oats, barley, turnips, broccoli, avocado, and beans.
    • Foods containing Resistant Starches: 

    Green or semi-green bananas, cooked and cooled potatoes, cooked and cooled rice, beans, and legumes.

      Tips to get more resistant starch from food: cooking potatoes or rice with a fat source like ghee or avocado oil dramatically increases the fraction of resistant starches formed upon cooling. In this way, starchy foods that typically cause large blood sugar spikes, like rice and potatoes, can be turned into functional foods that not only have lesser effect on blood glucose levels but that can also directly support the microbiome.

      The Best Prebiotic to Support Bifidobacteria

      Human milk oligosaccharides (HMOs) are the best prebiotic to support the growth of bifidobacteria in the gut. Although GOS, FOS, XOS can feed bifidobacteria, they also feed other types of bacteria like Lactobacillus and Lactococcus in the gut. Bifidobacteria will have to compete with them for the food.

      On the contrary, HMO is more selective for bifidobacteria. Bifidobacteria highly express the enzymes required to metabolize HMOs, making this prebiotic very effective at bolstering Bifidobacteria populations.

      [Check out this video to see how much Bifidobacteria were boosted by HMO in one man's experience.]

      Should You Take Prebiotics or Take Probiotics "Containing" Bifidobacteria?

      Unlike prebiotics which feed bacteria, probiotics are supplements containing key species of live bacteria that are believed to confer beneficial effects in the human gut.

      Although there are probiotics on the market that contain Bifidobacteria, the most effective way to increase their levels in the gut is through the use of prebiotics, not probiotics. This is because, in order for bacteria to grow and stay in the gut long term, proper nutrients must be present to support their growth.

      Moreover, most probiotics contain only a few billion organisms, which is a usually drop in the ocean compared to the total number of organisms in the gut.

      Therefore, consumption of prebiotics like HMOs, resistant starches, and polyphenols will naturally boost the residential Bifidobacteria populations in a way that is both more significant and more durable than just taking the Bifidobacteria cells that are inside most probiotic products on the market. 

       What other Factors Influence Your Bifidobacteria Levels?

      In addition to the influence of dietary components on Bifidobacteria populations, genetic factors also influence the levels of Bifidobacteria present in our guts.

      Specifically, antigen molecules secreted by our intestinal cells can serve as a food source for Bifidobacteria. Antigens are proteins or complex sugars that are recognizable by the immune system. However, 20% of individuals are unable to secrete these antigens due to mutations in the gene FUT2.

      This “non-secretor” phenotype is associated with significantly lower levels of Bifidobacteria in the gut and higher incidence of IBD, ulcerative colitis, and Crohn’s disease. Thus, it is imperative for non-secretors to consume even higher amounts of prebiotics than secretors in order to bolster their levels of Bifidobacteria and protect themselves from disease.

      [To learn more about FUT2 and how to determine your FUT2 status, read our previous blog post on the topic.]

      The Takeaway

      In summary, Bifidobacteria occupy a critical niche within the gut microbiome that not only promotes gut health by increasing overall microbial diversity, but also supports the production of butyrate.

      In addition to serving as the primary fuel source for colon cells, butyrate also modulates immune cell functions and decreases the levels of inflammatory factors produced. The attenuation of inflammation at both the level of the gut and the whole body is critical for disease prevention and healthy aging.

      Although there are genetic factors that can influence Bifidobacteria levels, the regular consumption of soluble fibers and prebiotics is a straight-forward and inexpensive strategy that anyone can use to increase Bifidobacteria presence in the gut.


      Written by: Dr. Alexis Cowan, a Princeton-trained PhD specializing in the metabolic physiology of nutritional and exercise interventions.

      Follow Dr. Cowan on Instagram: @dralexisjazmyn



      Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJM, Faber KN, Hermoso MA. Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol. 2019 Mar 11;10:277. doi: 10.3389/fimmu.2019.00277. Erratum in: Front Immunol. 2019 Jun 28;10:1486. PMID: 30915065; PMCID: PMC6421268.

      Wu X, Wu Y, He L, Wu L, Wang X, Liu Z. Effects of the intestinal microbial metabolite butyrate on the development of colorectal cancer. J Cancer. 2018 Jun 15;9(14):2510-2517. doi: 10.7150/jca.25324. PMID: 30026849; PMCID: PMC6036887.

      Henrick B et al. Bifidobacteria-mediated immune system imprinting early in life. Cell. 2021; 184(15).

      Wacklin P, Mäkivuokko H, Alakulppi N, Nikkilä J, Tenkanen H, Räbinä J, Partanen J, Aranko K, Mättö J. Secretor genotype (FUT2 gene) is strongly associated with the composition of Bifidobacteria in the human intestine. PLoS One. 2011;6(5):e20113.


      2 Responses

      Gama Xul
      Gama Xul

      March 09, 2024

      Great products. The Covid spike protein, either from vaccine or shed from the infected, can reduce your bifidobacteria to 0. Yes, Zero. And that causes all manner of dysfunctions and diseases in the body. Nearly all of human health begins in the gut so this is important to manage. Go with the natural foods avenue if you can’t afford the focused prebiotic supplements. We have to stay healthy.

      John LaBry
      John LaBry

      August 14, 2023

      I am suffering from Long COVID inflammatory response with continuing minor cramping in the gut (it was much worse for a few months after COVID), and a strong muscular inflammatory response after exercise. There was a study in Hong Kong that found that individuals with Long COVID had suffered a loss of bifidobacteria in the gut by as much as 50%. I’m thinking your products might help my condition, but it seems that the two products that would be most beneficial are out of stock. Can you say when they might be available again?


      Leave a comment


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