Friday Dec 1 | BY |
| No Comments

Microbiome Testing

We’re in the era of genomics. And, it’s easy to get a blueprint of your microbiome. Laboratory companies are selling gut microbiome screening tests on the internet direct to the consumer without a doctor’s prescription. But is it time for you to get your gut microbiome tested?

A January 2017 Consumer Reports write up advises to skip gut screening tests. But, my research and clinical experience suggest otherwise. The science and technology are excellent, and results are accurate. For example, uBiome has six issued patents and 73 others pending. Their advisory team of MDs and PhDs have published 20 scientific papers about gene sequencing.

The gut microbiome is an exciting field. It’s a crossway between conventional medicine and functional medicine.

Gut Microbiome Imbalances: A Pathway to Health or Illness

Our gut microbiome shapes our health, immunity, and metabolism. Microbial transformations occur in our colon that makes us who we are, affect our energy and mood, and defend us from infections and cancer.

Gastrointestinal disorders begin in the mouth. The food we eat ends in the gut as food for our microbes and benefits for us.

But not getting enough fiber, eating refined foods, overeating fast foods, packaged foods, and not consuming enough green vegetables are factors that affect the gut’s microbiome and our health. Improper cooking is another reason. Certain foods like dried bean have to be cooked a long time to break down inflammatory lectins. Otherwise, they cause gas and bloating. As can gluten sensitivity and milk allergy.

Many other factors contribute to gut imbalances, including aging.

As we age, our stomach lining atrophies. The cells that secrete gastric acid produce less hydrochloric acid. Low acidic levels allow Helicobacter pylori and other pathogenic bacteria to thrive.

Too many bad bugs trigger inflammation causing gastritis. They overflow the stomach into the small intestine causing fermentation. Too many bacteria can cause small intestine bacterial overgrowth (SIBO) associated with bloating and belly pain. Patients with SIBO complain that they look five months pregnant.

In the large intestine, microbiome imbalance is termed dysbiosis, describing an unhealthy shift in the gut microbiome composition. Chronic dysbiosis is considered a cause of IBS, autoimmune disorders, mood changes, weight gain, metabolic disorders, CFS, and colon cancer.

But, it’s not only a question of too many bugs. Gut bacteria imbalances count.

One of the most common imbalances is the ratio of Firmicutes species, making up most of the number of bacteria in the gut, and Bacteroides. The F/B ratio measure in a stool sample provides a gauge of overall gut imbalance.

In chronic fatigue syndrome (CFS) patients with irritable bowel syndrome (IBS), as well as older people, the F/B ratio tends to be low.

A 2009 study found that the F/B ratio changes with age. But is aging the only factor causing altered F/B ratio? Studies in Europe found that the F/B ratio was different between countries. This research suggests either a genetic variation or a dietary difference, or both.

A 2014 study confirmed that microbiome imbalances occur during aging but found that diet was the primary factor in determining gut bacteria. The most common decline was in Bacteroides, Lactobacillus, and Bifidobacterium.

Besides diet and aging, other causes of gut microbiome imbalance include sedentary lifestyle, high stress, excessive alcohol intake, and gut-damaging medications like antibiotics and ibuprofen.

Specialized Gut Flora Matter

Specialized gut bacteria like Faecalibacterium prausnitzii (also called Fusobacterium prausnitzii) a member of the Firmicutes phylum, play critical roles in health and disease. Higher levels of F. prausnitzii are associated with health. Lower levels of illness. This common bacterium produces butyrate and short chain fatty acids (SCFAs) necessary to maintain the gut lining. Low F. prausnitzii levels contribute to leaky gut, chronic inflammation in the gastrointestinal tract, and the whole-body symptoms associated with CFS like fibromyalgia pain.

Restoring Your Microbiota

Nutraceuticals or functional foods including prebiotics, probiotics, polyunsaturated fatty acids, amino acids, and polyphenols, help modulate the intestinal microbiota.

Viscous fiber in food has health benefits, but few functional fiber preparations are both practical and palatable. For my patients, I recommend the new viscous fiber supplement PolyGlycopleX (PGX). It’s an evidence-based functional food that beats old-fashioned fiber supplements like psyllium husks that can be hard on the intestines.

Five Ways to Restore Your Microbiome:

  1. Take a viscous fiber supplement.
  2. Avoid gluten and lectin-containing foods.
  3. Take probiotics that emphasize the beneficial bacteria Bifidobacterium and Lactobacillus.
  4. Take a digestive enzyme containing betaine hydrochloride and pancreatic enzymes with every meal to support digestion.
  5. Take hypoallergenic prebiotics to support growth of beneficial bacteria.

Probiotics, Prebiotics, and Symbiotics

Probiotics are live microorganism supplements. To be effective, enough have to reach the intestine in an active state. You have to take amounts in the billions of units, and you need ones that are alive and active.

Most health food marketplaces offer many probiotic products found in the refrigerated section. Choose those containing Lactobacillus rhamnosusLactobacillus reuteribifidobacteria species, strains of Lactobacillus casei, and Lactobacillus acidophilus.

A prebiotic is a natural ingredient that helps change the composition and activity of the microflora environment to benefit wellbeing and health. The most common prebiotics are inulin-type fructans, including fermentable chicory fructans. Some prebiotics contains corn and may cause allergic reactions to those sensitive to corn.

Synergistic combinations of probiotics and prebiotics are called synbiotics. One hypoallergenic synbiotic that I recommended to my patients is Microbiome Plus+. Another is HLC Synbiotic Intensive from Pharmax.

Several research reviews have summarized the benefits associated with probiotic supplements for older adults. Typical benefits include increased levels of bifidobacteria, improved bowel function with less constipation, enhanced innate immunity, and reduced inflammation.

How Probiotics and Prebiotics Benefit the Body

  • Improve digestive health
  • Improve nutrient absorption
  • Enhance immunity
  • Help prevent cancer
  • Increase calcium absorption
  • Improve detoxification
  • Lower inflammation

Some probiotics can reduce diarrhea caused by antibiotic use or overgrowth of potentially pathogenic strains of bacteria. Saccharomyces boulardii, a strain of yeast, which significantly reduces the incidence of Clostridium difficile-associated colitis.

What to Look for In a Microbiome Test

You can now test your gut microbiome without a doctor’s prescription. Look for ones that are evidence-based, easy to use, and affordable.

  • uBiome SmartGut
  • Biohm
  • MapMyGut (England)
  • DayTwo (Israel) is different from the others because it analyzes your microbiome to assess blood sugar response to foods predicting which ones are best for you.

When looking for the right microbiome test, I recommend the following three guidelines:

  1. A diversity score. Beside individual flora, the lab should provide an overall diversity score. Low diversity is associated with illness.
  2. Test for key flora. Tests should check for important populations of flora including Lactobacillus, Bifidus, Firmicutes, Bacteroides, and Faecalibacterium prausnitzii.
  3. An F/B ratio. The lab should calculate the ratio and present it in an easy to read manner on the test report. A low F/B ration is associated with illness.

Expert interpretation is always the key factor in any medical laboratory test. Learning on your own requires lots of reading and endless hours on the internet. A good lab will provide a Q&A brochure with your report. Some offer consulting services for an additional fee.

You might even find that a doctor experienced in microbiome testing is a valuable ally in your quest to regain your health, to prevent disease and stay well, and for ridiculously healthy aging.

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.

Visit Dr. Williams’ Website:

And Follow on Facebook:


Comments are closed.