How To Know The Biodiversity Of Your Microbiome

Friday May 22 | BY |
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microbiology biome microbiome biodiversity

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

What’s the most exciting frontier in modern medicine? According to Michael Pollan, author of In Defense of Food, it’s our microbiome. What’s a New York Times bestselling food journalist doing taking about bugs in his gut? Thousands of scientists, doctors, and personal health advocates agree, it’s the microbiome.

Our internal ecosystem is composed of a dazzling area of different kinds of bugs, worms, protozoa, fungi, and bacteria. Some of these can kill you, but most help keep our immune systems tuned up and our genes humming.

What is a microbe?
Two words – “micro” and “bios” – combined together mean small life. Microbes are living organisms so small that we can’t see them without a microscope. Microbiota is the colony of microbes that make up the human microbiome consisting of more than 100 trillion microbial cells.

Our Inner Compost Heap

I’m a lifelong gardener and beekeeper. Because I was raised on a small working farm in New England, 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. If we didn’t have enough from our own animals, we bought chicken manure from a local poultry farm. I got dirty, very dirty.

From farm 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.

A good farmer knows that, so doesn’t kill off all the worms in the field. In order to feed people, a good gardener cultivates soil and plants. The good farmer encourages worms to thrive, which helps grow healthy plants to nourish healthy people.

A good doctor also knows not to kill off all the bacteria in the gut. In order to feel well, we have to have a thriving gut microbiome.

As it turns out, bugs are good. Even bad ones have a purpose.
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 Kambucha really feed your microbiome? Did the trip you made to volunteer putting in 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 the 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. Any one, any where in the world can join and sign up for a swab kit.

Clinical Gut Testing Tools

For the average, healthy person under 45 years old, knowing the variety of the microbial population in your gut in a great start. However, older people and those with chronic disease need more information from their gut.

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.

If you have chronic illness, especially autoimmune and allergic diseases, you need specialized stool testing that includes butyrate, short-chain fatty acid levels, and other gut markers as provided by Genova and similar 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 view 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 also patients with gum disease, as well as cardiovascular disease get a swab test for bacteria in their mouths. OralDNA Labs and Dental DNA provide testing kits.

Clinical gut testing results may require the interpretation by a doctor or dentist knowledgeable in the clinical implications of an imbalanced microbiome.


Diet Counts

Your microbiome shifts in response to diet. When microbiome bacteria shift, so do your genes. When your genes shift in a negative direction, your health suffers.

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
  • High fiber, plant-based diet
  • Breast milk
  • Prebiotic foods like Jerusalem artichoke, onions, and garlic
Five Steps To Hack Your Microbiome:
  1. Get tested on your own to find out if you have enough microbial diversity.
  2. If you have an autoimmune or allergic disorder, get comprehensive testing from your doctor.
  3. Make changes in your lifestyle and diet.
  4. Take probiotics and prebiotics, or a combination of both called symbiotics.
  5. Retest every three months for one year.

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

Gut bugs even play a role in cancer prevention. Stool samples of people with colorectal cancer contain less of the bacterial groups Lachnospiraceae and Roseburia and more of Enterococcus and Streptococcus. Too much E. coli bacteria produce toxins that trigger DNA breakage. Instability in the genome is linked to the process that ends with tumors.

We’re still on the frontier of manipulation of the microbiome to treat disease, but there’s no reason that you can’t get tested now.

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. Deane Alban says:

    This is a fascinating topic! If I may add a point to the conversation, artificial sweeteners can affect your gut bacteria balance, too. One study found that the gut bacteria that thrive on artificial sweeteners are the very same ones shown to be particularly abundant in the guts of genetically obese mice. This may be one of the mechanisms by which diet soda makes people gain rather than lose weight.

  2. June Hanson says:

    When I first came to see Dr Williams was battling enterococcus & mrsa many Iv’s of antibiotics making me sicker, with G.I. problems His program and stool tests ordered, put me on right probiotics, prebiotics, changing diet, eliminating all sugars. Followed his instructions take supplements that really work. To say, I am thrilled at the change it has made in my quality of life, it putting it mildly. Highly recommend, following this blog. Cannot thank Dr Williams, for giving me back, my life.

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