How to Hack Your Astonishing Microbiome

Friday Dec 16 | BY |
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Doctor shows information: microbiome

What is the most exciting frontier in human science? Thousands of scientists, doctors, medical journalists, and natural health practitioners agree. It’s the microbiome.

Our body’s internal ecosystem is composed of a dazzling area of different kinds of microbes including bugs, worms, protozoa, fungi, and bacteria. Some of these can kill us, but most help keep our immune system tuned up and our genes humming.

What Is a Microbe?

Two words – “micro” and “bios” – combined mean small life. Microbes are living organisms so small that we can’t see them without a microscope. The term microbiota refers to the colonies of microbes that make up the human microbiome consisting of more than 100 trillion microbial cells.

Our Microbiome Is Huge

The genes of our gut microbes outnumber our own by 150 to 1. The human microbiome is the sum of all our microbial genes. And, that does not just include good ones. We are composed of a collection of friendly, neighborly, and dangerous microbes. Some of them cause disease and some can be deadly.

When the balance favors commensals and symbiotics, the friendly and neighborly microbes, we are healthy and have a sense of wellness. If the balance shifts towards pathogenic ones, we get sick.

Our microbiome is not only massive; it is highly diverse. Like a rainforest or coral reef, our health requires an endless array of microbes. When microbial diversity diminishes, we get sick.

A Good Doctor Is Like a Wise Farmer

I grew up on a small working farm in New England. So, I’m not squeamish around bugs. I collected worms for fishing. I shoveled tons of cow and horse manure that we spread on our hay fields and vegetable garden.

From farm boy to biology wasn’t a big leap for me. Thinking about the inner molecular world fascinated me as a student and still holds my clinical interest. In naturopathic medicine, we’ve been applying therapies for gut ecology decades before medical doctors showed an interest.

To feed people, a good gardener cultivates soil and plants. A wise farmer knows that a lush garden produces tasty vegetables, so doesn’t kill off all the worms in the ground. Agricultural practices that encourage worms to thrive help to grow strong, vital plants that nourish healthy people.


Like the wise farmer, a good doctor knows not to kill off all the bacteria in the gut. To feel well, we have to have a thriving gut microbiome.

But most conventional doctors detest bugs, which they call “germs.” However, just because some make us sick, doesn’t mean that all bugs are bad. The vast majority of microbes are integral to life on this planet and to your health.

Know Thy Gut with Crowd Science

Want to know if eating fried cicadas or grasshoppers will improve your gut biodiversity? How do you know if the probiotic supplements you’re taking are working? Does Kombucha feed your microbiome? Did the trip you made to volunteer to dig wells for impoverished Africans give your immune system a boost or knock it down? If you want to know, get tested.

Crowd science companies provide microbiome testing technology and generate infographics based on your results. See how you compare with others, and to groups including vegans, paleo dieters, and even in heavy alcohol drinkers. Most of these companies measure microbial populations in the gut, mouth, skin, and vaginal areas.

You don’t need a doctor’s prescription to test your microbiome. The San Francisco company uBiome uses DNA sequencing technology from a simple swab sample. Results provide a personal reference library of your microbes.

The American Gut is the world’s largest open source project to understand the human microbiome. Anyone, anywhere in the world can join and sign up for a swab kit.

Clinical Gut Testing Tools

To understand your general health, start with blood testing. Next, an overview of the variety of the microbial population in your gut is a great tool.

Clinically speaking, besides providing a record of your microbial genome, it is also necessary to discover essential metabolites and look for the presence of pathogenic organisms, like fungi, yeast, and parasites.

Microorganisms in the gut ferment dietary carbohydrates into a wide range of metabolites including short-chain fatty acids, propionate, and butyrate. Just knowing the biodiversity of your gut microbiome is not enough if you’re sick. You also need to know the by-products of bacteria metabolism.

If you have a chronic illness, especially autoimmune and allergic diseases, you need functional stool testing that includes butyrate, short-chain fatty acid levels, and other gut markers as provided by Genova Diagnostics and similarly licensed laboratories.

For my patients with chronic disease, microbiome and blood testing are the cornerstones of my clinical practice. My stool test of choice is GI Effects from Genova Diagnostics. This test provides a detailed overview of your gut bacteria, yeast and fungi, and common parasites, as well as metabolic and immunological markers associated with gut health.

Not only do I test the gut microbiome, but for patients with gum disease, I order a swab test for bacteria in their mouths. OralDNA Labs and Dental DNA provide testing kits.

Clinical microbiome test results may require the interpretation by a doctor or dentist knowledgeable in the clinical implications of an imbalanced microbiome. For example, if you have Chronic Fatigue (CFS) Syndrome, a pattern emerges in your results. You may find an imbalance of your metabolites. You likely will have an overall lower diversity of both number and types of gut bacteria.


Diet Counts

Want to know if eating fried cicadas or grasshoppers will improve your gut biodiversity? If you want to know what’s going on with your gut, get tested.

Your microbiome shifts in response to diet. When microbiome bacteria evolve, so do your genes. When your genes change in a negative direction, your health suffers. Guiding them back to balance promotes wellness.

Foods & Medicines That Knock Off Good Gut Bacteria:

  • Refined sugar
  • Trans fats
  • Tylenol (acetaminophen)
  • Antibiotics
  • Excess alcohol
  • Infant commercial formulas

Foods That Improve Your Gut Microbiome:

  • Fermented Foods
  • Natural organic yogurt and kefir
  • Plant-based diet
  • Adequate fiber
  • Breast milk
  • Prebiotic foods like Jerusalem artichoke, onions, and garlic

Probiotics and Nutritional Supplements Help

Our microbiome forms an essential part of our biology. It influences nutrition, immunity, and mood. Our inner bugs affect metabolism and produce at least 10 percent of our energy. They help make vitamin B12 and vitamin K2. Microbiome imbalances are linked to obesity and difficulty losing weight, as well as autoimmune diseases, allergies, IBS, and even cancer.

Scientists now know that the gut microbiome plays a central role in the brain-gut axis. A two-way information highway links your brain and gut. The key molecule of the brain-gut axis is serotonin. It is so important that most of the body’s serotonin is produced by the gut microbiome. Many specialized probiotic microbes produce serotonin.

Serotonin-Producing Bacteria:

  • Escherichia coli
  • Hafnia alvei
  • Klebsiella pneumoniae
  • Lactobacillus lactis
  • Lactobacillus plantarum
  • Streptococcus thermophilus

Researchers link low serotonin to depression, chronic pain, addiction, appetite control, and the lack of feelings of wellbeing.

Many common nutrients found in food are necessary to support a healthy microbiome. However, for those with IBS and CFS, supplements are required to improve gut integrity.

Researchers found that Lactobacillus helveticus R0052 and Bifidobacterium longum RO175 reduce anxiety and improve mood. Vitamins B2, B12, vitamins D3 and K2, and serotonin precursors like L-tryptophan and 5-HTP are necessary for a healthy gut microbiome. Though known to promote healthy sleep, melatonin supports serotonin levels and is good for brain and gut.

Seven Steps to Hack Your Microbiome:

  1. Get tested to find out if you have enough microbial diversity.
  2. Cut out refined sugar and add fermented foods.
  3. Take probiotics and prebiotics according to your test results.
  4. Add L-Tryptophan and like 5-HTP to support serotonin.
  5. Take Vitamin B2 to keep the mucosal lining of your gut in good shape.
  6. Retest every three months for one year. Make adjustments along the way.

As it turns out, most bugs are good. Even some bad ones have a purpose. But, we are still on the frontier of manipulation of the microbiome to treat disease. However, there is no reason that you cannot get started right now on your path to wellness. Get a stool tests to find out about your gut microbiome.

Dr. J. E. Williams


Dr. Williams is a pioneer in integrative and functional medicine, the author of six books, and a practicing clinician with over 100,000 patient visits. His areas of interest include longevity and viral immunity. Formerly from San Diego, he now resides in Sarasota, Florida and practices at the Florida Integrative Medical Center. He teaches at NOVA Southeastern University and Emperor’s College of Oriental Medicine.

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  1. June Hanson says:

    Am so glad you take care of my microbiome. Put me on just the right probiotics, prebiotics, correct vitamins, minerals, many supplements that keep me healthy. Also very thankful you do not have me eating grasshoppers! Your knowledge, growing up on a farm, sparked something within you, to give you such wisdom on this subject. Having IBS all my life, no one able to help me, you have given me new life. Thank You.

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