Microbiome Primer

Microbiome Primer
Laura Krauss MS, RDN
Clinical Dietitian


What is the microbiome?

According to the human microbiome project, the microbiome is “the collection of all the microorganisms living in association with the human body… Bacteria in an average human body number ten times more than human cells, for a total of about 1000 more genes than are present in the human genome. Because of their small size, however, microorganisms make up only about 1 to 3 percent of our body mass (that’s 2 to 6 pounds of bacteria in a 200-pound adult). These microbes are generally not harmful to us, in fact they are essential for maintaining health.”

Why is it important?

These microbe residents in our body serve a number of functions.

  • Produce vitamins: specifically the B vitamins and vitamin K
  • Breakdown food: increase our digestive capacity
  • Play a pivotal role in the immune system: 70% of the entire immune system is located in the gut
  • Keep bad bacteria at bay: by competing for space in the intestines, as well as producing substances that kill bad bacteria and producing natural antibodies
  • May alter our disease risk: a “healthy” microbe pattern in associated with normal weight, reduced risk for diabetes/insulin resistance, better cardiovascular health, better mental health and overall decreased risk for chronic disease.

How can we support its health?

  • Increase fiber:
    • Soluble fiber: AKA food for your microbes. As they eat, the microbes will produce short chain fatty acids, such as butyrate, that nourish the cells of your intestines.
      • Prebiotics: found in starchy tubers (potatoes, sweet potatoes), oats, apples, pears, flax and chia seeds, onions/garlic. In supplemental form, look for fructans, inulin, fructooligosaccharides (FOS), arabinogalactans
      • Resistant starch: lesser known fiber found in cooked and cooled starchy foods like plantains, potatoes, green bananas and rice.
    • Insoluble fiber: helps to move stool out of the digestive tract, but does not “feed” the microbes. Found in the peels of fruits and vegetables, leafy greens and whole grains.
  • Decrease sugar and refined carbohydrates: these are the bad bugs favorite foods to chow down on.
  • Eat fermented foods: these types of foods contain live bacteria. The most accessible one is yogurt (plain is your best option), but fermented veggies like raw sauerkraut and kim chi are also good options. Other options are kefir, coconut kefir and kombucha tea. Probiotic supplements are also an option if you are dealing with a gastrointestinal disorder or suspect gut imbalances (like with skin issues, allergies or autoimmune disorders).
  • Avoid unnecessary antibiotics: remember that antibiotics cannot distinguish the good bugs from the bad. If you must take antibiotics, keep your microbe population in mind when you make food choices and consider adding a probiotic supplement or increasing your intake of fermented foods.

For more information on the microbiome visit:

Human Microbiome Project

Human Food Project

For $99 you can sequence the genome of your microbiome through American Gut!

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