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A Healthy Gut Microbiome

The gut is like a garden...

When we take antibiotics we lose the good bacteria in our garden. We have bad bacteria grow like weeds, such as C. difficile colitis and other multi-drug resistant organisms. Our goal in our therapeutics is to restore health by replanting that garden with fecal transplants. Our research is now to figure out the components of the natural gut garden that promote health and well-being. 

Everyone is talking about a healthy gut microbiome, and for good reason!  


Found in your lower intestine (your colon), the gut microbiome contains trillions of active bacteria working for your health.  This microbiome has been described as an organ and ecosystem with over 400 different types of bacteria.  Everyone has their own unique microbiome made up of different types and amounts of bacteria.  Depending on the bacterial diversity and composition, the microbiome could influence your health.

But what makes a gut microbiome healthy?

Protective bacteria help keep your gastrointestinal (GI) tract intact and help to digest fiber and absorb needed nutrients.  Cells called epithelial cells line the GI tract and serve as an important barrier.  In an ideal world these cells rest tightly next to each other, creating tight junctions.  These tight junctions provide a barrier protecting your body from outside bacteria, much like your skin does on the outside of your body.  Researchers think that bacteria called Firmicutes and Bacteroidetes help protect and strengthen these cells.  When this balance gets disturbed (dysbiosis), the junctions between the cells can loosen causing bacteria to travel from the intestines into the body.  This loosening of junctions causes gut permeability.


Some researchers believe that your gut bacteria composition depends on the types of nondigested food parts or fiber that make it to your colon.  Fiber, or non-digestible carbohydrates, is often referred to as prebiotics.  It seems that a bacteria’s growth and strength in the gut depend on whether or not they have competition for food. An important thing to remember is that you want protective bacteria to be fed with the foods that you eat.  If you do not supply them with the food they need, some protective bacteria could die and some of aggressive bacteria could begin eating from your own cells in the gut.  This could cause dysbiosis as well as gut permeability. 


what Conditions affect the microbiome?

  • Inflammation

  • Cardiovascular Disease

  • Chronic Fatigue

  • Metabolic Syndrome

  • Antibiotic use

  • Stress

  • Alcohol intake

  • Exercise

  • Disease status


Currently, the relationship between the gut microbiome and disease is being explored.  Some connection has been shown with certain illnesses, however, exactly what this means for the bacteria make-up of the microbiome is not yet known.  Those illnesses and diseases include


  • Clostridium difficile (C. diff )

  • Inflammatory Bowel Disease (IBD)

  • Irritable Bowel Syndrome (IBS)

  • Auto-Immune Diseases

  • Obesity


To make this even more complicated, the amounts and types of bacteria that you have in your gut make you unique.  Yours will look different from your neighbor, from your family, and from someone in another part of the world.  The bacteria numbers and diversity can change because of how you were born and additional factors beyond your control, but other influences on the microbiome are due to lifestyle.  Factors that influence the gut bacteria survival and composition include

  • Your environment

  • How you were born - vaginally or by C-section

  • As an infant, were you breastfed or formula fed?

  • Genetics

  • Age

  • Diet

How can i improve my gut health?

Although no one can say for sure exactly what your gut microbiome should be, you can do a few things to help give yourself the best possible scenario for your microbiome:


  1. Limit antibiotic use, if possible

  2. Reduce stress

  3. Exercise regularly

  4. Limit alcohol intake

However, your diet choices can make a huge difference in giving your gut bacteria what they need.  Although many companies have products such as prebiotics and probiotics, food seems to be the best starting source for these components.


  1. Singh, R.K., et al., Influence of diet on the gut microbiome and implications for human health. J Transl Med, 2017. 15(1): p. 73.

  2. Cresci, G.A. and E. Bawden, Gut Microbiome: What We Do and Don't Know. Nutr Clin Pract, 2015. 30(6): p. 734-46.

  3. Mills, S., et al., Precision Nutrition and the Microbiome, Part I: Current State of the Science. Nutrients, 2019. 11(4).

  4. Makki, K., et al., The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host Microbe, 2018. 23(6): p. 705-715.

  5. Rinninella, E., et al., What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms, 2019. 7(1).

  6. Malikowski, T., S. Khanna, and D.S. Pardi, Fecal microbiota transplantation for gastrointestinal disorders. Curr Opin Gastroenterol, 2017. 33(1): p. 8-13.

  7. Lazar, V., et al., Gut Microbiota, Host Organism, and Diet Trialogue in Diabetes and Obesity. Front Nutr, 2019. 6: p. 21.

  8. Sonnenburg, E.D. and J.L. Sonnenburg, Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab, 2014. 20(5): p. 779-786.

What is a healthy gut microbiome?

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