The microbiome continues to dominate the research front.  That 5 pounds of microbial life that inhabits our digestive tract is far more responsible for our health, most people would ever guess.  It’s composition and how various populations of microbes relate to one’s risk of particular conditions is being intensely studied.  While some of the research surrounding specific microbiome profiles (diversity, presence of larger families of bacteria, or the numbers of potentially pathogenic strains for instance) is preliminary and limited to associations, many microbiologists and microbial experts believe that there is a great deal we can now say with confidence.

First, diversity is paramount.  This is essentially an ecosystem. We are ultimately talking about an ecosystem with an incredible amount of control over our gene expression, neurotransmitter production, and hormone balance, as well as those systemic processes that rely on immune system recruitment and inflammation.  With greater diversity, meaning more families of commensal bacteria, the microbiome can continue to support good health even when faced with a unique challenge or exposure.  A course of antibiotics, a less than ideal meal nutritionally, or a bout of the flu, may have some short-term consequences but we soon recover and have no long lasting effects.  Without diversity, these same exposures can create chronic health issues.

Second, there is really good evidence that some families of bacteria need to be kept in check. Smaller numbers of these potentially pathogenic strains will be well tolerated with the aforementioned diversity, but if their numbers start to increase because of conditions created by diet: look out.  Such is the case with Clostridia and Klebsiella families of bacteria and Candida within the yeast/fungal World.  These are the usual suspects when patients suffer from chronic diarrhea, Crohn’s disease or ulcerative colitis, or thrush with Candida infections.  How does the landscape of the microbiome become ripe for the overgrowth of these organisms? Sugar.

Some sources of sugar are worse than others with respect to fostering the overgrowth of pathogens (1).  Those foods and beverages, or in the enteral area-formulas, contain much of their sugar in the form of fruit sugar or fructose.  Fruit juice, fruit juice concentrates, and high fructose-containing fruits are often the leading ingredient and foundations for enteral formulas.  Many formulas that claim to be made of whole foods and are marketed as blender-ized derive a major percentage of their calories from fruit sugar.  Recent investigations in this area of human metabolism would suggest that it is a poor choice of calories when we assess how the liver and our risk for insulin resistance are affected (2,3).  Now there are also lines being drawn that connect disease-causing bacteria populations within the microbiome to diets rich in sugar, specifically fructose (4,5).

Preventing dysbiosis or overgrowths of pathogens in our gut revolves around eating less sugar and more vegetables.  Even the amount of sugar from fruit and fruit juice causes health issues (6).  Most people do not eat enough vegetables and vegetable fiber that comes with them.  Enteral formulas tend to look a lot like the typical American meal: low in vegetables, high in fruit sugar.  Why would we feed patients an enteral formula that looked similar to the foods that we know make others sick or that have been shown to cause issues with a person’s microbiome?  It just doesn’t make sense.  Of course you should also avoid those that contain omega 6-rich seed oils, emulsifiers, and the herbicide glyphosate as these have consistently been shown to eliminate the most beneficial families of bacteria (7,8,9).  Heat processing a formula does not eliminate glyphosate or other agrichemicals, so be sure that your foods and formulas are glyphosate-tested.

Functional Formularies produces enteral formulas with no fruit, fruit juice, or any other added source of sugar.  This is the only enteral formula in the World that can say this.  What have the studies conducted with Liquid Hope shown?  The microbiome of animals fed Liquid Hope are more diverse.  There are far greater levels of commensal or beneficial bacteria with animals fed Liquid Hope and the numbers of pathogenic strains are markedly lower (10).  In summary, when it comes to the microbiome and supporting its health, choose foods and formulas wisely by avoiding fruit juice-laden products and finding those built on organic vegetables.

 ~ John Bagnulo MPH, PhD.




1. Sabag-Daigle A, Wu J, Borton MA, et al. Identification of Bacterial Species That Can Utilize Fructose-Asparagine. Atomi H, ed. Applied and Environmental Microbiology. 2018;84(5):e01957-17. doi:10.1128/AEM.01957-17.

2. Lambertz J, Weiskirchen S, Landert S, Weiskirchen R. Fructose: A Dietary Sugar in Crosstalk with Microbiota Contributing to the Development and Progression of Non-Alcoholic Liver Disease. Frontiers in Immunology. 2017;8:1159. doi:10.3389/fimmu.2017.01159.

3. Crescenzo R, Mazzoli A, Di Luccia B, et al. Dietary fructose causes defective insulin signalling and ceramide accumulation in the liver that can be reversed by gut microbiota modulation. Food & Nutrition Research. 2017;61(1):1331657. doi:10.1080/16546628.2017.1331657.

4. Zubiría MG, Gambaro SE, Rey MA, Carasi P, Serradell M de los Á, Giovambattista A. Deleterious Metabolic Effects of High Fructose Intake: The Preventive Effect of Lactobacillus kefiri Administration. Nutrients. 2017;9(5):470. doi:10.3390/nu9050470.

5. Ferrere G, Leroux A, Wrzosek L, et al. Activation of Kupffer Cells Is Associated with a Specific Dysbiosis Induced by Fructose or High Fat Diet in Mice. Guillou H, ed. PLoS ONE. 2016;11(1):e0146177. doi:10.1371/journal.pone.0146177.

6. .  Sara J White, Emma L Carran, Andrew N Reynolds, Jillian J Haszard, Bernard J Venn; The effects of apples and apple juice on acute plasma uric acid concentration: a randomized controlled trial, The American Journal of Clinical Nutrition, Volume 107, Issue 2, 1 February 2018, Pages 165–172.

7. Kaliannan K, Wang B, Li X-Y, Kim K-J, Kang JX. A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia. Scientific Reports. 2015;5:11276. doi:10.1038/srep11276.

8. Dudek-Wicher RK, Junka A, Bartoszewicz M. The influence of antibiotics and dietary components on gut microbiota. Przegla̜d Gastroenterologiczny. 2018;13(2):85-92. doi:10.5114/pg.2018.76005.

9. Mao Q, Manservisi F, Panzacchi S, et al. The Ramazzini Institute 13-week pilot study on glyphosate and Roundup administered at human-equivalent dose to Sprague Dawley rats: effects on the microbiome. Environmental Health. 2018;17:50. doi:10.1186/s12940-018-0394-x.

10. Original presentation: Whole-Food Enteral Nutrition Prevents Gut Dysbiosis and Improves Outcomes in a Mouse Colitis Model. Society of Academic & Research Surgery (SARS) Annual Meeting, January 7-8, 2019 in London.