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Gut Microbiome Health from Supplements

by Michael Cutler, M.D.

Your intestinal health is predominately controlled by the kinds of bacteria, yeast and viruses residing there, which subsequently impacts virtually all systems in your body. In this article, let’s look at the supplements proven to improve your delicate gut microbiome balance.


Optimal gut health is found when there is a wide range (high diversity) and a high quantity of healthy bacteria ("probiotics”). The lactobacilli and bifidobacteria strains have been most studied. In the past 5 years, strains of healthy bacteria have been identified and studied using DNA sequencing.  

The general rule I use for identifying a good probiotic to purchase is one with 20 Billion colony-forming units (cfu) per capsule or more, and one that can survive stomach acid to get to the large intestine. It will take at least two months of daily supplementation to establish colonization in and near the large intestinal tissue wall.

Probiotics have also been proven to protect from adverse effects of antibiotics, which are known to disrupt your gut microbiota.[i]  Even short-term antibiotic treatment is known to shift a healthy gut microbiota to create a long-term dysbiotic condition. In one study, healthy volunteers who were treated for up to 1 week with antibiotics reported symptoms of adverse effects of bacterial flora which persisted 6 to 24 months after treatment. They were found to have a dramatic loss in bacterial diversity, increased antibiotic-resistant strains, and upregulation of antibiotic resistance genes.[ii]

Unfortunately, even one single dose of Clindamycin (antibiotic) has been shown[iii] to induce profound changes in the gut microbiota of mice even to consequently confer long-lasting susceptibility to C. difficile infection.

Furthermore, surveys on thousands of children have shown a link between the use of antibiotics in the first year of life and asthma development by 6 to 7 years of age.[iv]


Prebiotics are foods or supplements that feed the healthy gut bacteria. When healthy gut bacteria digest (ferment) prebiotic fibers, it produces short-chain fatty acids such as butyrate, acetate and propionate which are an important fuel for intestinal epithelial cells to strengthen the gut barrier function.

Some prebiotic supplements include fructo-oligosaccharide (FOS). Another is human milk oligosaccharide (HMO).  

Some prebiotic foods are high-fiber foods including vegetables, fruits, seeds and grains such as chicory root, dandelion greens, garlic, onions, leeks, asparagus, bananas, berries, flax seeds, and barley.

Bacteriophage viruses

The most cutting edge supplement to aid in intestinal health are bacteriophages (a.k.a. phages). With recent science of DNA sequencing, certain phages are proven by in vitro and placebo-controlled clinical studies to:

  • increased beneficial bacteria,[v] including Bifidobacterium bifidum and Lactobacillus delbrueckii
  • influence the microbial population of the gut by increasing butyrate-producing Eubacteria. These short chain fatty acids (SCFAs), in particular butyrate, also have important immunomodulatory functions[vi]
  • have positive effects on cholesterol and immune response
  • show significant decrease in the allergy-inducing interleukin 4 (IL-4) cytokine

Some peer-reviewed study authors explain that, “The viral component of the human gut microbiome is dominated by bacteriophages (phages), which are known to play crucial roles in shaping microbial composition, driving bacterial diversity, and facilitating horizontal gene transfer.”[vii]  Also, “While antibiotics can cause or exacerbate microbiota imbalances or dysbiosis, phages offer the opportunity to subtly and selectively modify the gut microbiota.”[viii]

Taking eating prebiotic foods often and daily supplements containing probiotics, prebiotics and bacteriophages in combination, you’ll have the best success at achieving and maintaining a healthy gut microbiome to reduce chronic inflammatory disease.

To a healthy gut microbiota and long life,

Michael Cutler, M.D.

[i] Hathaway-Schrader JD, Steinkamp HM, Chavez MB, Poulides NA, Kirkpatrick JE, Chew ME, Huang E, Alekseyenko AV, Aguirre JI, Novince CM. Antibiotic Perturbation of Gut Microbiota Dysregulates Osteoimmune Cross Talk in Postpubertal Skeletal Development. Am J Pathol. 2019 Feb;189(2):370-390. PubMed PMID: 30660331.

[ii] Jernberg C, Löfmark S, Edlund C, Jansson JK. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 2007 May;1(1):56-66. PubMed PMID: 18043614.

[iii] Buffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, Viale A, Ubeda C, Xavier J, Pamer EG. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun. 2012 Jan;80(1):62-73. PubMed PMID: 22006564.

[iv] Kozyrskyj AL, Ernst P, Becker AB. Increased risk of childhood asthma from antibiotic use in early life. Chest. 2007 Jun;131(6):1753-9. PubMed PMID: 17413050.

[v] Febvre HP, Rao S, Gindin M, Goodwin NDM, Finer E, Vivanco JS, Lu S, Manter DK, Wallace TC, Weir TL. PHAGE Study: Effects of Supplemental Bacteriophage Intake on Inflammation and Gut Microbiota in Healthy Adults. Nutrients. 2019 Mar 20;11(3):666.. PMID: 30897686. 

[vi] Parada Venegas D, De la Fuente MK, Landskron G, González MJ, et al. 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. PMID: 30915065. 

[vii] Sutton TDS, Hill C. Gut Bacteriophage: Current Understanding and Challenges. Front Endocrinol (Lausanne). 2019 Nov 29;10:784. PMID: 31849833.

[viii] Francino M.P. Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front. Microbiol. 2016;6:1543.

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