Love Your Microbiome

Dr. Joel Ying, MD

Physician, Educator, Storyteller. He hosts this website for "Living the Present Moment" as a conscious journey of Body, Mind, Emotion & Spirit. Holistic and integrative, his practice includes Tai Chi and Yoga, Craniosacral Therapy, Healing From the Core, Meditation. Always exploring his edges, he shares them in the blog, newsletter, courses, and online study group.

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When I began studying alternative medicine more than a decade ago, the word “probiotics” was on the fringe. Probiotics are good bacteria that live in a normal gut. They can help re-populate the gut after an illness or when antibiotic disrupts the normal balance of bacteria. There was controversy about whether they were more than placebo. Now every mainstream doctor has heard the term, and they can even write a prescription for them. (You can still get them over the counter as well.)

Is it “us” versus “them”? Can we move past anti-biotics — the war on bacteria?

The bacteria and viruses that inhabit the cells that we call “us” are often beneficial to and essential to the life we live. Yes, an imbalance of the wrong type of bacteria or virus in the wrong place can cause problems that we call “infection.” In this case, we may need the anti-biotics.

The cells that are not “us” outnumber “us” by more than 10 to 1. Their genes outnumber ours 100 to 1. Perhaps we are just here for them. Perhaps we are here for each other.


The term “microbiome” has now become mainstream. This is the natural “flora” of organisms (including bacteria) that live in our gut to help with digestion or live on our skin to help as a barrier of protection or other areas of the body. Researchers now study the microbiome as an organ (a group of cells that serve an essential body function). Different areas of the body have a different balance of microorganisms.

How do we keep our microbiome healthy?

  • Antibiotics disrupt the microbiome by attacking both good and bad bacteria. If you need to take antibiotics, you will need time to build up your microbiome.
  • Avoid taking unnecessary antibiotics.
  • Take antioxidants and herbals for immune support when needed. Sometimes you can avoid antibiotics.
  • Probiotics can support your microbiome. There are different versions and different strains.
  • Fermented foods that contain probiotics can also support the microbiome.
  • Antibiotic soaps have recently been taken off the market because they have not shown benefit in preventing infection (or imbalance) with bad bacteria. They are not any more helpful in most cases than regular soap and water. They also likely disrupt the health of the microbiome of our skin.

It is a difficult transition to reorganize our thinking of what “clean” means. “Clean” for our skin does not mean no bacteria. “Clean” for our gut definitely does not mean no bacteria. Without the normal gut flora, we would not be able to digest our foods properly, we would not be able to extract all the nutrients, and we would not be healthy.

A healthy microbiome can prevent “infection”. Yes, there are virulent super strains of bacteria and viruses that take over and grow in the wrong place leading to an imbalance of flora that we would call infection. But why is it that not everyone gets sick when they come in contact with someone sick. We all have an immune system that also keeps the balance of organisms in check, keeps the balance between us and them. A healthy immune system needs adequate nutrients and rest. If your body is run down or over-stressed, the immune system will not have the energy to keep you healthy. Keep your body healthy by supporting your immune system, supporting your microbiome, and supporting balance within your system. The war mentality of “us” against “them” is outdated when it comes to maintaining wellness, the optimal word is balance. Health is balance for body, mind, and spirit.

C. diff Colitis

A super-virulent strain of C. diff bacteria has become resistant to cure with the traditional treatment of antibiotics. This bacteria produces a toxin that causes a severe inflammation of the colon, severe pain and diarrhea, and can lead to death in severe cases. The overgrowth of this bacteria is often tipped off by antibiotic exposure that kills the good bacteria in the gut. Other antibiotics are then used for C. diff infection, but the super-virulent strain is resistant to these antibiotics. Researchers are currently studying a therapy of “stool transplant” or rePOOPulation or other equally creative names for this therapy to cure this infection by re-establishing the microbiome of your gut. Yes! By using the microbiome of a healthy donor. I will leave it to your imagination how that gets done.

Love your microbiome

It’s an organ for health, and needs to be balanced.

Watch this fun video “The invisible universe of the human microbiome” from NPR.