Healthy Microbiome: Gut Check

Do you have a healthy microbiome? How can you find out? Why does it matter?

Bacteria, viruses, fungi and other microscopic living things are referred to as microbes. Trillions inhabit your mouth, nose, eyes, ears, digestive tract, lungs, skin and genitals.

Scientists estimate that there are more bacterial cells in your body than an average male adult’s 30-40 trillion human cells. However, our microbes only weigh two to five pounds! Most are in your gut.

There are thousands of species of bacteria in the human gut microbiome which play a role in our health or lack of health. It is mostly a symbiotic relationship. They keep us alive by:

• • protecting us against germs
  • breaking down food to release energy
  • producing vitamins

We keep our microbiome thriving by providing food, warmth and our living host environment. After our death, most species in our microbiome die within two days. The rest help consume us.

Research is showing that a healthy microbiome also likely protects us against obesity, diabetes, heart disease and cancer and that the gut microbiome may affect the central nervous system, which controls brain function.

It is not surprising to find out that our bacteria control aspects of our mood and behavior.

There are several ways to test and analyze your microbiome. Direct to consumer microbiome test companies include:

• Biohm $194.99 USD
• Floré $299 USD
• My Med Labs $399 USD
• Ombre $119.99 USD
• Viome (gut) $279 USD or (full body) $199/month plus precision supplements)– see Keep Health’s review.

Innerbody Research reviewed the above vendors in 2024. Viome is their top recommendation.

Microbiome testing companies available only through your physician include:

• Diagnostic Solutions Lab 
• Doctor’s Data 
• Genova Diagnostics

Once you have your microbiome baseline, you can use these 15 ways to boost it and then re-test to see if there was beneficial change. Additionally, some people choose to supplement with prebiotics and probiotics, especially during and after using antibiotics. Most antibiotics only wipe out some of your microbiome.

Failed Microbiome Companies

• Atlas Biomed (London) 
• Finch Therapeutics — Conducted trials to attempt to treat Recurrent C.difficile infections, a dangerous gut infection which defies current antibiotics. They achieved an 80%+ cure rate in Phase 2. However, Phase 3 was discontinued. The history of Finch and other C.diff therapeutic companies is quite fascinating as they attempted to turn poop into profits.
• Kaleido Bioscience declared bankruptcy amidst $360 million in outstanding debt. Among multiple mistakes, they believed their microbiome therapy was a food and not a drug. They initiated expensive trials under this premise that were not cleared by the FDA. The FDA rejected them with this warning letter. Microbiome therapeutics need to play by the same rules as regular drugs.
• Synlogic — Attempted to create “living medicines” based on gut bacteria to target brain and liver disorders. Primary focus was a Phase 3 clinical trial for engineered probiotic strain to lower blood Phe levels for Phenylketonuria patients. It did not achieve its primary endpoint.
• Ubiome suspended operations after a federal investigation for fraudulent billing practices. They were providing skin, nose, gut, oral and genital tests for $400 for 4 samples / year.

Probiotics are supplements of  live bacteria and yeasts intended to provide health benefits when consumed by improving digestion and maintaining gut health as well as improving brain function. They are considered generally safe, but in rare cases may cause bacteria-host interactions and unwanted side effects.

The effectiveness of probiotics varies from person to person. Probiotics face a daunting challenge to survive stomach acid and their interactions with trillions of potentially hostile microbes. Since probiotic pills are merely billions of microbes, they are a tiny amount of intruders relative to their competitive environment. Also, new bacteria require specialized food and may starve without it. Thus, taking probiotics with prebiotics (food for probiotics) may be necessary. Here is Healthline’s list of the best 19 prebiotic foods.

There are nineteen companies selling prebiotic and probiotic supplements which have been tested by Consumer Labs. Only Dr. Ohhira’s Probiotics was not approved. Here are a few with reputable science and scientists behind them.

• Seed is backed by a Scientific Advisory Board of leading expert scientists, researchers, doctors, and authors across the fields of microbiology, immunology, genetics, metabolomics, pediatrics, gastroenterology, molecular biology, and transcriptomics—including primary investigators from the NIH’s Human Microbiome Project. They  teach at world-renowned academic institutions, and have among them 2800+ publications and over 140,000 citations in peer-reviewed scientific journals and textbooks.
• Seed also wins in the clever marketing department. Once ordered, they send you an email letting you know that, “We got your bac. And it’s on its way to you.”

• Provides a targeted blend of probiotics and prebiotics, personalized by your Viome Gut Health scores.
• Contains probiotics and prebiotics from this extensive full potential ingredient list.

Although you might not think reading about microbes would be interesting, we highly recommend the New York Times bestseller,  I Contain Multitudes, a clever, fascinating and fun book about insights into life. Once you start reading it, your microbes will make it very hard to put down.

Additionally, you might enjoy David Ewing Duncan’s The Voyage of Sorcerer II, chronicling Craig Vinter’s global exploration to retrieve and sequence the ocean’s microbiome. This brings to life the modern day version of Darwin’s expedition. Did you know that:

• the planet Earth should actually be renamed to Water since the oceans contain 130 million liquid cubic miles.
• phytoplankton provide 50-80% of the oxygen on Earth.
• bacteria began to produce oxygen 3-4 billion years ago.
• the estimated number of bacteria on Earth, err Water, is 5000000000000000000000000000000. (thirty zeros).
• it is fine for scientists to have fun while pursuing meaningful research.