Microbiome Testing: Not What You Think It Is

When you spend that $89 or $99 or even $499 on a gut biome test, you are participating in an ambitious research program aimed at learning more about the human gut.   If you are parting with your money in the belief that you are going to learn something about your own health, you may be very disappointed.   Because gut biome science is currently in its infancy; meaning scientists have begun ask great questions about the human gut, but are far from arriving at any answers.

And scientists have a lot to learn about your gut health. The human body consists of dozens of trillions of cells but only 10% of those cells are human.  The other 90% is comprised of more than 100 trillion microorganisms that symbiotically sustain many of our bodily functions…including good gut health.  Without, there is no us. Only with the advent of lower-cost generation sequencing in 2005 were scientists able to begin studying microbiota in the human GI tract, also referred to as the microbiome.

What scientists are beginning to learn is promising.  For example, some scientists have discovered even the slightest imbalance in our microbiome may lead to disease. Antibiotic use appears to have decreased bacteria diversity in lab animals’ guts, leading to observable obesity problems. Other scientists have noted a difference in bacterial diversity between microbiomes of healthy children compared to the autistic ones. Intriguing, but they don’t know what or how to “fix” these potential imbalances.  That’s because the medical profession’s understanding of the “normal” microbiome patterns, including what constitutes a healthy versus diseased pattern is still in its infancy. Only a few associations have been established in human studies thus far.

Commercial Gut Biome Testing

So, we have a promising but data-poor area of scientific study.  Medical entrepreneurs see the opportunity (and value) in finding high-quality, low-cost data to help feed scientists’ studies and they’ve seized upon selling gut microbiota kits.   Building upon the data mining strategies of Google, Microsoft and Facebook, some Israeli and US-based start-ups have begun offering microbiome testing for anywhere between $89-$400.   These tests will help identify microorganisms, but they can’t diagnose gut conditions.  Some of these companies may supply you with customized lifestyle advice to maintain a healthy microbiome, but don’t be fooled into thinking that you are getting a medical consultation.  And even if the tests are being sent to your MD,  your doctor wouldn’t be able to tell you more than whether you have a serious bacterial infection.   The following chart, posted in greater depth at dnatestingchoice.com shows some of the companies offering these tests to consumers:

Another new startup, Thryve, began offering a monthly microbiome testing subscription service in February 2017 starting at $59.95 a month. The company claims to use machine learning to generate customized reports showing the breakdown of a person’s gut bacteria. Their reports also give advice like which fibrous foods to eat or probiotics to drink to improve “good” bacteria. Customers have access to an online platform with a chatbot that asks them questions about what they ate that day and whether they exercised or took dietary supplements.

If you do choose to have your microbiome scanned, you will receive a kit in the mail that contains sterile swabs and instructions on how to collect samples from stools or, in some cases, your tongue or skin. Once you’ve mailed the sample in and it has been analyzed, you’ll get a list of the dominant microbial species populating your gut.   Each of the companies provide different information, but most will offer lists of various bacteria along with their relative prevalence, percentage-wise, in the sample from your gut.   But most of this information is relatively useless for an untrained eye.

“You’ll get an enormous amount of data that is basically uninterpretable,” Dr. Martin J. Blaser, director of the Human Microbiome Program at New York University told the NY Times.  However, he added, “there are people who will be very happy to take your money and tell you they can interpret it.”  Another expert echoes Dr. Blaser:  “The enthusiasm of their manufacturers simply goes well beyond where the science is right now,”according to Rob Knight, a leading microbiome researcher and professor at the University of California, San Diego.

Consumer Reports recently reviewed these various financial tests and arrived at the same conclusion.  Do these tests work:  Their answer is: “we don’t know. Microbiome research has made impressive strides and promising developments in recent years. Scientists have identified hundreds of common intestinal microbes and have begun linking at least some of them to specific symptoms and conditions. But one of science’s golden rules is that correlation doesn’t equal causation. That is, showing that two things are linked isn’t the same thing as proving that one caused the other.”

Like so many unbiased observers, Consumer Reports concludes that there simply not enough scientifically validated research to determine whether specific gut microbes are responsible for certain health conditions.  And we are even further away from building from this new evidence of causation to get to actual treatments that are safe and effective for humans.  As quoted in MIT Technology Review, Jack Gilbert, faculty director of the Microbiome Center at the University of Chicago, says it might be possible to find out how the microbiome is affecting a person’s disease or make tailored dietary recommendations, but it would require much more data and monitoring over several months or even years. For companies to do that well, he estimates, it would cost consumers $5,000 to $6,000, not $400.  That’s because the scientifically valid method of studying gut biomes is to observe such changes would be in a long-term study where people are enrolled before they get sick.  But that’s a much more costly process.

“This is a relatively young field, so you always have to be careful with the possibilities for translating these findings,” said Mount Sinai Icahn School of Medicine microbiome researcher Jose Clemente, whose lab is in discussions with a number of companies interested in using microbes to treat IBD.  Like Gilbert, he believes it may not be enough to consider gut microbes alone, but also interactions with their hosts, which may be driven by individuals’ genetics and susceptibilities to certain conditions.

Some consumers have expressed concerns that they’ve essentially paid money to be part of a much larger study.  One such consumer noted on Amazon:  “I purchased the gut kit directly from uBiome and after finding out that the test is processed differently if you don’t agree to take part in their program where they sell your data (won’t see any info regarding this until you go to register the kit) I stumbled upon a lot of unhappy people that after 3 months of waiting tye have yet to receive any data. I requested a refund because of this and that i didn’t finish the registration so that couldn’t keep the money anyways because it was to perform a test not the kit.”

So you must go into microbiome testing with an understanding that this is a massive but creative data mining effort.  Your information is being used for a larger purpose than just giving you copious amounts of largely unusable data.  As for those consumers looking to making lifestyle changes, most people probably don’t need a microbiome test to tell them to eat healthier.  So you needn’t fork out a few hundred dollars, unless you feel you need the kick in the butt needed to improve your food selection.

So What Do Scientists Really Know Right Now?

If you’ve decided to take the tests, here is some information that might be useful in your interpretations of the data dump you’ve received.  Thus far, scientists have gleaned some condition/bacteria correlations, but understand that much, if not all, of this information will be subject to revision or rescission in the coming years:

  • The gut microbiome of Americans and most other Westernized, industrialized populations is less diverse and dominated by different bacterial species than that of people from rural, less developed populations. Diet plays a role, but a general shift away from natural environments with little exposure to soil, animals, and other environmental microbes seems to be impacting the gut microbiome in potentially detrimental ways.
  • In fact, diet seems to be the most powerful influence of the gut microbiome. Processed foods containing emulsifiers and detergent-like compounds may damage the intestinal lining, potentially leading to “leaky gut” and systemic inflammation (contributing to inflammatory-based diseases such as diabetes and CVD). Fibers – including food-based resistant starch, soluble fiber and insoluble fiber are some of the key nutrients for promoting fermentation and ensuring a diverse microbiome. Such non-digestible dietary components are known as prebiotics, which stimulate the growth or activity of the gut microbiota.
  • Most researchers agree that the lack of fiber in the Western diet is harmful to the microbiome. Others add concerns about the additives in processed foods, few of which have ever been studied for their specific effects on the microbiota. According to a recent article in Nature by the Stanford microbiologist Justin Sonnenburg, “Consumption of hyperhygienic, mass-produced, highly processed and calorie-dense foods is testing how rapidly the microbiota of individuals in industrialized countries can adapt.”
  • Children raised in homes with pets have less risk of allergic diseases and new evidence is demonstrating a link with gut microbiome patterns. Exposure to dogs seems to alter the gut microbiome to be protective against allergic airway issues and respiratory viruses. So, Lucy Van Pelt may have been wrong to condemn Snoopy’s kisses.
  • Most probiotic products that are commercially available to consumers have not been investigated for effectiveness. Furthermore, there are no standard formulas or dosages and some probiotic formulas include bacteria that may be beneficial for some problems, but not others. It’s interesting to note that when NY Times journalist and best-selling author, Michael Pollan asked the top experts in the field of microbiome research about their use of probiotics, most do not take them, but rather focus more on a whole-foods diet rich in prebiotic items and fermented foods.
  • “Normal” gut microbiota in healthy persons include such pathogenic strains as E. coli and Enterococci, which are both linked to serious intestinal disease.  Scientists haven’t been able to distinguish which are good versus the bad bacteria, or if some have both roles.
  • H. pylori the microbe that Western medicine has actually been trying to exterminate it since 1983, when Australian scientists proposed that the microbe was responsible for peptic ulcers, might actually be an important part of microbiotic health.  Scientists learned that H. pylori also plays a role in regulating acid in the stomach. Presumably it does this to render its preferred habitat inhospitable to competitors, but the effect on its host can be salutary. People without H. pylori may not get peptic ulcers, but they frequently do suffer from acid reflux. Untreated, this can lead to Barrett’s esophagus and, eventually, a certain type of esophageal cancer, rates of which have soared in the West as H. pylori has gone missing.
  • Antibiotic therapy alters the patterns of gut microbiota and when given early in life (infancy and childhood) may shift the bacterial profile towards one that promotes obesity, metabolic abnormalities and/or autoimmune diseases. This relationship is seen in livestock animals given low-dose antibiotics to enhance growth and weight gain, so this relationship in humans is also being explored.  One recent study found that when subjects were given a second course of antibiotics, the recovery of their interior ecosystem was less complete than after the first.   Bottom line: avoid antibiotics when possible.
  • Most of the microbes that make up a baby’s gut community are acquired during birth — a microbially rich and messy process that exposes the baby to a whole suite of maternal microbes. Babies born by Caesarean, however, a comparatively sterile procedure, do not acquire their mother’s vaginal and intestinal microbes at birth. Their initial gut communities more closely resemble that of their mother’s (and father’s) skin, which is less than ideal and may account for higher rates of allergy, asthma and autoimmune problems in C-section babies. So, the microbes that latch onto you as you pass through the birth canal may be so important to your health later on that they’ve been looking into whether—and how—those microbes could be given to babies born via C-section.
  • Research has linked the microbiome to a growing list of conditions, including obesity, Parkinson’s disease, and depression.  Again, there’s not enough data to determine which bacteria are the culprits, if any at all.
  • Studies have linked human microbes to a myriad of health conditions, noted a report from the University of Utah, including acne, antibiotic-related diarrhea, asthma/allergies, autism, autoimmune diseases, various cancers, dental cavities, depression and anxiety, diabetes, eczema, gastric ulcers, atherosclerosis, inflammatory bowel disease, malnutrition, and obesity.
  • Our gut bacteria also play a role in the manufacture of substances like neurotransmitters (including serotonin); enzymes and vitamins (notably Bs and K) and other essential nutrients (including important amino acid and short-chain fatty acids); and a suite of other signaling molecules that talk to, and influence, the immune and the metabolic systems.
  • Researchers also report that humans cannot survive without their microbes. Bacteria genes aid in human digestion and absorption of nutrients that otherwise would be unavailable, according to  Lita Proctor, Ph.D., HMP program manager at the National Human Genome Research Institute (NHGRI) in a NHGRI press release.
  • Microbes in the gut break down many of the proteins, lipids and carbohydrates in our diet into nutrients that we can then absorb and these microbes also produce beneficial compounds, like vitamins and anti-inflammatories that our genome cannot produce—some of which are anti-inflammatories that regulate some immune system responses to disease, such as swelling.

For more authoritative resources about microbiome research,  we urge you to check out the Knight Lab at UCSD, the Center for Microbiome Innovation and the Translational Microbiome Research Forum.   They are pretty amazing resources, albeit somewhat technical.

1 reply
  1. Rdenny
    Rdenny says:

    Your info on microbiome testing was invaluable for me. It’s definitely opened my eyes to some things. I’d not appreciated how science really hasn’t figured out gut biomes yet. Please keep up the good work for all of us.


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