We often think of bacteria as something bad, something that will make us sick, something we need to get rid of, but as we are now learning, good bacteria is essential for our bodies to stay healthy and free of disease. If you read Part One of our Gut Microbiome discussion, you know that we are mostly bacteria, that our bacteria are constantly sending messages to the brain and the body, and if we have bad bacteria, it can wreak havoc on our health, our mood, and just about every function in our body.

Good vs. Bad: The goal is to have diversity of good bacteria in our gut. One of the biggest problems we face in trying to maintain a healthy gut microbiome is that antibiotics have been overprescribed. While they are absolutely necessary in many cases and do destroy the bad bacteria, antibiotics alter the gut microbiome by destroying healthy bacteria as well. Studies have shown that after one 7-day course of antibiotics, there can be long term negative changes in the gut bacteria, even up to two years later. These changes create an inflammatory state in the body which can lead to insulin resistance, diabetes, obesity, and the list goes on…

Other things that negatively affect our good microbes are:

  • Artificial sweeteners
  • Refined sugars
  • Gluten
  • NSAIDs
  • Antacids (i.e. Tums) and proton pump inhibitors (i.e. Nexium and Prilosec)
  • Chemicals often found in tap water such as chlorine and fluoride

How does the bad bacteria in our intestines create inflammation in the rest of the body? If we are not getting adequate amounts of fiber (prebiotics), the membrane of the intestines breaks down and allows toxins from the G-I tract, to leak into the bloodstream (Leaky Gut). Inflammation results in response to these “invaders”. If we continue to eat foods that do not feed our good gut bacteria, we leave our body vulnerable to being in a chronically inflamed state.

Help! Let’s not get caught up in the weeds; how do we improve our microbiome? You can improve your gut in as little as 24 hours just through diet and exercise

Adding probiotics (good bacteria) and prebiotics (fiber that feed the good bacteria) can make a significant impact. Simply put,

  • Go for a walk
  • Get rid of the sugar
  • Add some fermented foods
  • Increase your fiber intake

Below is a list of some popular and palatable foods you can eat to improve your “second brain”. Also try to vary your healthy foods to create diversity in your gut microbiome.


  • Avocados
  • Broccoli
  • Brussel Sprouts
  • Asparagus
  • Artichokes
  • Legumes
  • Onions
  • Berries


  • Sauerkraut
  • Kim Chi
  • Kefir
  • Lamb
  • Kombucha
  • Kosher pickles
  • Olives
  • Apple Cider Vinegar

You may also want to consider a probiotic supplement. Our favorite is Dr. Ohhira Probiotics. , with ingredients that are fermented for 3-5 years, and contains prebiotics and probiotics. However, we recommend you get advice from your physician about any supplement products.

A few small changes in your diet and activity level can make huge changes in your health now and in the future. Many allergies, ailments and diseases can be helped by cleaning up your gut issues first. Create your own platform for health through your gut microbiome.


If you’re interested in learning more, here are some books on the subject that are worth checking out:

Missing Microbes – Martin J. Blaser, MD

The Good Gut – Justin Sonnenburg and Erica Sonnenburg, PhDs

The Microbiome Diet – Raphael Kellman

Lastly, if you’re thinking about having your gut microbiome tested, here is a company we’re currently researching:  https://viome.com/