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The New Endangered Species: The Human Gut Microbiome

gut microbiome, colon health, gut health

By Dr. Mercola

The documentary film ‘The Invisible Extinction’ shares why modern-day life is decimating the human microbiome, threatening its diversity and human health in the process. 

  • The film “The Invisible Extinction” warns that the human microbiome is endangered, putting humans at risk.
  • The film highlights the work of microbiologists Dr. Martin Blaser and Gloria Dominguez-Bello — a husband-wife team — who are looking into both the problem and a potential solution to save microbial diversity.
  • The overuse of antibiotics, elective C-sections, and processed foods are “driving the destruction of our inner ecology,” according to the film.
  • The dramatic increases in chronic diseases, including Type 1 diabetes, asthma, obesity, gastroesophageal reflux disease, and inflammatory bowel disease, may be linked to the loss of bacterial diversity in our guts.
  • Dominguez-Bello is president of The Microbiota Vault, a global nonprofit initiative attempting to “conserve long-term health for humanity” by storing and preserving microbiota samples and collections.

The documentary film, “The Invisible Extinction,” is sounding the alarm that the human microbiome is endangered, putting humans at risk. “Bacteria have been the dominant life form on Earth. Everything about human life depends on bacteria,” the film begins.1

Researchers are only beginning to tap the surface when it comes to unveiling the complex relationship microbes have with human health and disease. But it’s known that microbial diversity in your gut is a good thing, while decreased diversity in the gut microbiome has been linked to chronic conditions such as obesity and Type 2 diabetes.

In general, gut microbial diversity decreases with age,2, but even younger people are being affected. The documentary homed in on three likely reasons why — the overuse of antibiotics, elective C-sections and processed foods, which they say are “driving the destruction of our inner ecology.”3

Making a Mess of Microbial Diversity

The film highlights the work of microbiologists Dr. Marty Blaser and Gloria Dominguez-Bello — a husband-wife team — who are looking into both the problem and a potential solution to save microbial diversity. In explaining why he chose to focus the film on the research of Blaser and Dominguez-Bello, after speaking with many microbiologists, co-director, and producer, Steven Lawrence explained to Sloan Science and Film:4.

“Marty’s research, which is quite broad, defines the problem, whereas Gloria’s looks for the solution — whether it’s preserving indigenous people’s microbes, thinking about how we can make c-section births less detrimental in the long term, in addition to advocating for fewer elective c-sections. 

“There are people around the world doing important, foundational research, which will hopefully filter down into a much more nuanced view of what it means to be healthy. We can all be healthy physically but have very different microbiomes; there is a protectiveness in diversity within ourselves as well as within our species, and I think that’s what Gloria’s work on the microbiota vault [discussed below] is about.”

The microbiome refers to all the microbes that live in and on your body. Not only does it play a role in digestion, but it’s also foundational to immune system function. In fact, your gut microbiome affects nearly all your physiological systems.

In my interview with Rodney Dietert, Professor Emeritus of immunotoxicology at Cornell University, he explains that we’re microbial beings, as “more than 99% of your genes are from microbes, not from your chromosomes.”5 You have approximately 3.3 million microbial genes, mainly bacterial. Across the entire population of humans, there are just under 10 million different microbial genes, so you won’t necessarily have all of them.

You also have 22,000 to 25,000 chromosomal genes (these genes were analyzed through the Human Genome Project), meaning you only have about 2,000 more chromosomal genes than an earthworm. As noted by Dietert, since we have about 3.3 million microbial genes, that means we’re more than 99% microbial, genetically.

Yanomami Indigenous People Most Microbially Diverse

Research by Dominguez-Bello and Blaser involved characterizing the fecal, oral, and skin bacterial microbiome of the Yanomami, an isolated group of indigenous people who live in the Amazon rainforest. In a study published in Science Advances in 2015, they wrote:6 “These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group.

Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity …”

By studying the microbiomes of these indigenous people, Dominquez-Bello believes we can gain clues as to what functions are lost in urban areas, where modern lifestyles are putting the microbiome at risk. In an interview with People, she explained:7

“These are peoples that are only now starting to be exposed to urban practices and medicine. So these are survivors because you can imagine the mortality in places where there’s no medicine. If you fall from a tree, you are dead. If you break a leg, you are dead.

One of every ten mothers that are in labor, one mother or baby dies. So if you survive, you are really a survivor. And these are healthy people because the unhealthy ones have died. So we are very interested in understanding their microbiome. And what we find is that they have much higher diversity. In general, diversity is a marker of health. The more diverse the microbiome, the healthier the ecosystem.”

Why C-Sections May Be Robbing Babies of Microbes

The film also tackles cesarean section (C-section), which alters infants’ microbiota since they’re not exposed to their mother’s vaginal microbiota during birth. C-section delivery is associated with an increased risk of immune system and metabolic disorders, possibly due to altered microbes.

Research by Dominguez-Bello and colleagues revealed, however, that “vaginal seeding” of C-section babies successfully restores maternal microbes in the infant when done immediately after birth, naturalizing their microbiota.8 While it’s unknown if restoring the babies’ microbiota after birth leads to long-term health outcomes, Dominquez-Bello intends to find out. She told People:9

“If a baby is born via elective C-section, with no water breaking, they are not exposed to the mother’s microbiome in the vagina. But we have shown that if we normalize, at least partially, the microbiome of a baby that is born by elective C-section by rubbing them with gauze soaked in fluid with their mother’s microbiome, we can normalize the mouth microbiome of the baby during the first year of life.

Are we protecting kids against asthma, against Type 1 diabetes, against celiac disease, allergies, and obesity by doing this? We are doing a 5-year clinical trial to find out.”

Early-Life Exposures May Be Key to Disease Prevention

Regarding early-life exposures, it’s also been suggested that abnormalities with the gut microbiome early in life could play a role in autism. Blaser told People:10

“We know that the rate of autism has gone up dramatically over the last 80 years. And it’s a disease of early life — it manifests within the first couple of years. And so, we are interested in the idea that the early life microbiome, as it forms, has a connection with the brain.

We know that the microbiome is talking to the brain. And so, a number of investigators have been interested in the idea that maybe an abnormal early life gut microbiome is having an altered conversation with the brain, and it’s changing brain development.”

Acute lymphoblastic leukemia (ALL), the most common type of childhood cancer, may also have a microbial link, according to Melvin Greaves of the Institute of Cancer Research in London, U.K.11

Greaves’ study suggests exposure to microbes in early life may be the ticket to preventing ALL, which can be done through:

  • Vaginal delivery (versus cesarean)

  • Breastfeeding

  • Going to daycare as a baby

  • Exposure to older siblings

Past research supports these suggestions, including a 2002 study that found children who spent more time in daycare had a significantly reduced ALL risk.12 Breastfeeding was also associated with a reduced risk of ALL, whereas the introduction of formula within 14 days of birth was positively associated with ALL, as was exclusive formula feeding to 6 months.13

Antibiotics Are Decimating the Human Microbiome

Every year, about ten doses of antibiotics are prescribed for every person on Earth. Even children take a mean of 2.7 courses of antibiotics by age 2 and 10.9 by age 10. However, exposure often begins even earlier, as more than half of women receive antibiotics during pregnancy or shortly after birth.

“This is in addition to an unknown level of exposure from agricultural use of antibiotics,” Blaser explained in the Cleveland Clinic Journal of Medicine in 2018.14

 He believes that the dramatic increases in chronic diseases, including Type 1 diabetes, asthma, obesity, gastroesophageal reflux disease, and inflammatory bowel disease, are linked to the loss of bacterial diversity in our guts — caused by the overuse of antibiotics:15

“Before modern times, microbes were transferred from mother to child during vaginal birth, from the mother’s breast during nursing, through skin-to-skin contact, and from the mother’s mouth by kissing.

Now, widespread cesarean delivery, bottle-feeding, extensive bathing (especially with antibacterial soaps), and especially the use of antibiotics have changed the human ecology and altered the transmission and maintenance of ancestral microbes, which affects the composition of the microbiota.

The microbes, both good and bad that are usually acquired early in life are especially important since they affect a developmentally critical stage.”

In comparison to the Yanomami people in the Amazon jungle, who have high bacterial diversity, people in the U.S. have already lost 50% of their microbial diversity.16 This is why the risks of antibiotics must be carefully weighed against the benefits prior to use — and the use of antibiotics in the food supply must also be significantly reduced.

Processed Foods Destroy Your Microbiome

Another assault on your microbes comes in the form of processed foods. Fiber is “the single most important component of the diet to feed the microbiome,” Dominquez-Bello says,17, but it’s largely absent in processed foods. Chemicals in the food supply, such as the herbicide glyphosate, also disrupt microbes.

Consumption of whole foods is linked to higher gut microbiota diversity,18 as is consuming herbs and spices. Consuming capsules of spices — specifically cinnamon, oregano, ginger, black pepper, and cayenne pepper — favorably affected gut bacterial composition after just two weeks.19

 In another study, the diversity of gut bacteria increased after four weeks of consuming herbs and spices in three-fourths teaspoon or 1.5 teaspoon daily doses.20

In addition to herbs and spices, consuming fermented foods is another solid strategy for optimizing the health of your gut microbiome. A study assigned 36 adults to consume a diet high in fermented foods or high-fiber foods for 10 weeks. Those consuming fermented foods had an increase in microbiome diversity as well as decreases in markers of inflammation.21

The issue is that many Americans do not consume these healthy whole foods on a regular basis, instead consuming processed junk foods devoid of fiber and nutrients and packed with additives. Artificial sweeteners have also been found to alter gut bacteria in adverse ways.22

The Microbiota Vault

Dominguez-Bello is president of The Microbiota Vault, a global nonprofit initiative attempting to “conserve long-term health for humanity”23  by storing and preserving microbiota samples and collections. The idea is to maintain a bank of microbes that could be used to restore human microbiota as it gradually becomes less diverse — or, in the event it essentially goes extinct. Dominquez-Bello explained to People: 24“We need to preserve the current biodiversity of microbes in humans of everywhere. And this is also true for the environment. We are making a complete mess of biodiversity, including microbial. Microbes are essential in every ecosystem, not only in humans, animals, or plants but also in the oceans. The impact of human activities links together the whole thing.

We need to preserve microbes because they really modulate the functions of Earth … They modulate everything. They modulate our own gene expression. So there has to be more of that effort to preserve microbial biodiversity, to restore, because we will need restoration.”

In the immediacy, in addition to avoiding elective c-sections, consider the following to protect your microbiome as much as possible:


  • Eat plenty of fermented foods — Healthy choices include lassi, fermented grass-fed kefir, natto (fermented soy), and fermented vegetables.

  • Take a probiotic supplement — If you don’t eat fermented foods on a regular basis, a probiotic supplement can be useful.

  • Boost your soluble and insoluble fiber intake, focusing on vegetables and seeds, including sprouted seeds.

  • Get your hands dirty in the garden — Exposure to bacteria and viruses in the soil can help strengthen your immune system and provide long-lasting immunity against disease.

  • Open your windows — Research shows opening a window and increasing natural airflow can improve the diversity and health of the microbes in your home, which in turn benefit you.25

  • Wash your dishes by hand instead of in the dishwasher — Research has shown washing your dishes by hand leaves more bacteria on the dishes than dishwashers do. Eating off these less-than-sterile dishes may decrease your risk of allergies by stimulating your immune system.26


  • Antibiotics, unless absolutely necessary. If you use them, reseed your gut with fermented foods and/or a high-quality probiotic supplement.

  • Conventionally-raised meats and other animal products, as CAFO animals are routinely fed low-dose antibiotics.

  • Chlorinated and/or fluoridated water — This includes during bathing or showering.

  • Processed foods — Excessive sugars and otherwise “dead” nutrients feed pathogenic bacteria. Food emulsifiers such as polysorbate 80, lecithin, carrageenan, polyglycerols, and xanthan gum may have an adverse effect on your gut flora.

  • Agricultural chemicals, glyphosate (Roundup) in particular, is a known antibiotic and could potentially kill many of your beneficial gut microbes if you eat foods contaminated with it.

  • Antibacterial soap as it kills off both good and bad bacteria and contributes to the development of antibiotic resistance.

Disclaimer: The entire contents of this article are based upon the opinions of Dr. Mercola unless otherwise noted. Individual articles are based upon the respective author’s opinions, who retains copyright as marked.

This information is not intended to replace a one-on-one relationship with a qualified healthcare professional and is not intended as medical advice. It is intended to share knowledge and information from the research and experience of Dr. Mercola and his community. Dr. Mercola encourages you to make your own healthcare decisions based on your research and in partnership with a qualified healthcare professional. 

If you are pregnant, nursing, taking medication, or have a medical condition, consult your healthcare professional before using products based on this content.


Check out our Discover Blog for more fantastic articles by Dr. Mercola and many more lifestyle experts! 

Dr. Mercola

Dr. Joseph Mercola is a physician and New York Times best-selling author.

He was voted the 2009 Ultimate Wellness Game Changer by the Huffington Post and has been featured in several national media outlets including Time magazine, LA Times, CNN, Fox News, ABC News, the Today Show and The Dr. Oz Show.

His mission is to transform the traditional medical paradigm in the United States into one in which the root cause of disease is treated, rather than the symptoms.

In addition, he aims to expose corporate and government fraud and mass media hype that often sends people down an unhealthy path.

Sources and References

  1. The Invisible Extinction, Trailer, 0:11
  2. Aging (Albany NY). 2019 Jan 31;11(2):289–290
  3. The Invisible Extinction, Synopsis
  4. Sloan Science & Film May 11, 2022
  5. Bitchute, Microbiome and the Immune System, Interview with Rodney Dietert, Ph.D. January 22, 2021
  6. Science Advances April 17, 2015
  7. People January 3, 2023
  8. Cell Press August 13, 2021
  9. People January 3, 2023
  10. People January 3, 2023
  11. Nat Rev Cancer. 2018 May 21
  12. Br J Cancer. 2002 May 6;86(9):1419-24
  13. Nutr Cancer. 2015;67(3):431-41
  14. Cleveland Clinic Journal of Medicine December 2018, 85 (12) 928-930
  15. Cleveland Clinic Journal of Medicine December 2018, 85 (12) 928-930
  16. Cleveland Clinic Journal of Medicine December 2018, 85 (12) 928-930
  17. People January 3, 2023
  18. Int. J. Mol. Sci. 2019, 20(8), 1835
  19. The Journal of Nutrition, Volume 152, Issue 11, November 2022, Pages 2461–2470, doi: 10.1093/jn/nxac201, Intro
  20. The Journal of Nutrition, Volume 152, Issue 11, November 2022, Pages 2461–2470, doi: 10.1093/jn/nxac201
  21. Cell July 12, 2021
  22. Gut Microbes. 2015; 6(2):149–155
  23. The Microbiota Vault
  24. People January 3, 2023
  25. ISME Journal 2012 Aug;6(8):1469-79
  26. Pediatrics February 23, 2015