Curebiome Naturopathic

The Microbiome 101

microbiome, gut bacteria

microbiome, gut bacteria

Maybe you’ve been hearing this word flying around, and you’re wondering what it is or what it has to do you with. “Microbiome” is a term that came out of the Human Microbiome Project, a major research initiative started by the National Institutes of Health. The purpose was to understand the how changes in the microbiome affect human health. But what exactly is it?

The microbiome is the collection of microorganisms that inhabit every surface, nook and cranny that we have. Microorganisms include bacteria, fungi, viruses and other teeny tinies that live on and in us. These microbes inhabit our skin, mouth, lungs, genitals, and most important our gut.

As the initiative went on and study results came back it was clear that there is a lot more microbes than human to us. It’s estimated that for every 1 human gene there are 100 microbial genes. Many have gone to calling us a super-organism because of this, and for good reason.

So what does this mean for us? Most important is the discovery that we rely on our collective microbiome every day. Functions like digesting food and making neurotransmitters that affect mood and mental function. It also trains the immune system and fends off infectious diseases. There are many other benefits and plenty yet to be discovered.

One of the biggest things that comes from this research is that we can’t go on with killing microbes indiscriminately. Whether in the environment or our bodies with antibiotics. Disruption of the microbiome is a major contributor to health problems that we face in developed countries. These same health problems are often nonexistent in undeveloped countries. Diabetes, obesity, allergies and autoimmune diseases all have connections to a mistreated microbiome.

New connections are made every day with one thing clear, our microbiome works for us in countless ways when it’s healthy. If an imbalance in our microbiome occurs we risk problems like diabetes, autoimmune diseases, obesity and infections like the cold, flu or worse.

  • So what are the best ways to nurture our microbiomes?
    • Diet is the king, and one of the biggest factors in microbiome health. Diet creates a positive shift in hours to days. It increases the number of beneficial microbes and decreases the harmful (less beneficial) ones.
      • A good diet for your microbes contains plenty of fiber especially insoluble fiber – found in garlic, onions, jerusalem artichokes and many others. Some of these insoluble fibers are prebiotics which means they feed our good microbes.
    • Probiotics are also important. Probiotics are the actual microbe that is beneficial usually in a capsule form. You can find natural probiotics in fermented foods like yogurt, kefir, kombucha, kimchi and others.
      • An easy way is to pick up a quality probiotic supplement which “seeds” good microbes, and works especially well with diet.
    • Get outside. There is a completely different composition of microbes found in indoor air compared to a forest or beach. Spending time in nature gives you a dose of fresh air that’s good for your microbiome too!
  • What are the most common ways we disrupt and harm our microbiome?
    • Antibiotics are the a major culprit, and we’re talking specifically about
      • Unnecessary prescriptions,
        • Avoid these by asking your doctor if antibiotics are completely necessary or if the infection/condition will likely clear up on it’s own. If you need them take them, but antibiotics have no positive impact on viral infections like the flu or cold so make sure you need them.
      • Hand sanitizers, and
        • Avoid these by getting antibiotic free soaps and avoid using soaps you’re unsure about.
      • Agricultural antibiotics used to encourage weight gain in livestock.
        • Buy your foods, meats especially, organic whenever possible.
    • Poor diet
      • Diets that tend to push the microbiome the wrong way are high in processed foods like sugars, refined flour pastas or breads, and low in fiber.
    • C-sections
      • It might seem strange but newborns are seeded with bacteria as they pass through the birth canal. These bacteria are specially adapted to babies first food, milk. Emergency C-sections save lives, but elective C-sections are unethical and set a child up for a rough start.


  • The microbiome is our collection of microbes that bring us many benefits and protect us from numerous diseases.
  • This microbiome outnumbers our human genes 100 to 1 and our human cells 10 to 1.
  • It functions to help us digest foods, train our immune system, discourage infections, and much more.
  • We can encourage a healthy microbiome by
  • Eating plenty of veggies, fiber and fermented foods in place of sugar and other refined foods.
  • Taking probiotics
  • Getting outside
  • Taking antibiotics only when necessary
  • Avoid hidden antibiotics in soaps and in many non-organic meats


  1. Great video on the microbiome basics

Test your microbiome here