The Human Microbiome

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Our lives depend on the bacteria, fungi, and other microbes working in harmony within our microbiome.

New Research Points to Its Critical Role in Health and Disease

“One of these days – not tomorrow, but I hope not in the distant future – we will sample the microbiome of every child the first time his parents bring him to the doctor.”  Katherine Lemon MD, Harvard Medical School 

Would you believe it! There are 100 trillion of them, yet we’ve only just started to meet them. Trillions of bacteria, fungi, viruses, and some archaic critters that appeared not too long after the Bug Bang, live in us, on us, and literally for us. These bugs, collectively known as our ‘microbiome’, envelope us in a cloud as we move through space and gently collide with everybody else’s cloud, and they outnumber our own cells by ten to one (some say maybe only three to one, but heck, what’s a trillion more or less in this unfathomable interior universe!) They make up between three and five pounds of a person’s body weight. No two people on Earth have the same combination or diversity, not even identical twins, and sometimes the same group of bugs will perform different tasks in different people.

“When we are born, we are not alone,” says Spanish researcher, Professor A. Moya. “We already have different bacterial species that are interacting with our human cells. They are not independent, trying to survive in our gut, they are forming something like a superspecies.”

This life sustaining presence in us changes throughout our lives, but as long as the diversity of those trillions is high, we are healthy and our immune systems can handle life’s disasters. (Side note: Families with dogs and cats, especially the ones who sleep with their animals and allow dog slobber, have far higher microbiome diversity among their members than those without pets.)

Here’s one story to illustrate the power of the  microbiome: A man was medically treated for years for a chronic ear infection, without success. One day, he decided to scrape the wax out of his healthy ear, and stuff it into the infected one. It cured the infection and totally freaked out his physician, Dr. Andrew Goldberg, who saw this as a “Eureka moment [when] I realized that this patient was the perfect experiment: a good ear and a bad ear separated by a head. That guy wasn’t crazy; he was right. Clearly, he had something protecting one ear that he then transferred to the other ear. Drugs didn’t cure him. He cured himself.”

The Link Between Obesity and Intestinal Bacteria

Some bacteria can change from healthy to toxic during a person’s different life stages. For example, H. pylori works to protect the body from disease early in life, and helps to regulate body weight. But around a person’s middle age, H. pylori becomes a microbe that can cause ulcers and gastric cancer. Historically, H. pylori has been with us for millions of years, but due to the overuse of antibiotics along with widespread consumption of genetically modified foods, the H. pylori bacterium is now on the brink of extinction. This greatly concerns Dr. Martin Blaser, an international expert on this bacterium, who has shown that the world obesity epidemic is directly connected to the eradication of H. pylori. In his book, The Missing Microbes: How Killing Bacteria Creates Modern Plagues, he comments: “We will need to make sure that pregnant women have the appropriate microbial communities to pass on to their children. If they don’t, we will have to give them to the kids after they are born. Then … at the age of thirty or forty, they could go to a clinic and have them eradicated. That way, people can get the benefit of these organisms in early life without having to pay the cost as they age.” He suggests that the complete eradication of these ancestral microbes would be a public health disaster.

Possibly the most important service provided by the body’s microbiome is to ‘educate’ the immune system about how to recognize pathogens that must be killed.  Not only do many microbes educate our immune systems’  T-cells, others have ‘Pattern Recognition Receptors’ that allow them to sort the microbial billions into who belongs, who doesn’t, and who should be here or someplace else.

The obesity enigma becomes truly bizarre when considering the research study that showed the following outcome: Lean mice were given a random sample of microbes from obese mice, and the slim ones became fat even without a dietary change.

In fact, so much research has now been done on obesity and the microbiome that space does not permit a detailed discussion here, so we are saving that for the forthcoming July/August issue of Vitality.

“I would like to lose the language of warfare,” said Julie Segre of the National Human Genome Research Institute. “It does a disservice to all the bacteria that have co-evolved with us and are maintaining the health of our bodies.”  Our disregard for our resident microbes has caused virtually all the current health epidemics, almost all mediated through the use of antibiotics in medicine and food.

How Your Microbiome Can Increase or Decrease Your Risk of Disease

Our lives totally depend on those microbial trillions working in cooperative harmony. Indeed, all animals depend on their various microbiomes.  Alligators have their distinct microbiome, as do dolphins, spiders and birds. When our resident microbes are prevented from doing their complex interdependent activities they trigger or actually cause (here comes the short list!) every known inflammation-based condition, including:

  • asthma
  • arthritis
  • multiple sclerosis
  • autism
  • malnutrition
  • obesity
  • cancer
  • depression
  • anxiety
  • celiac disease
  • acne
  • gastric ulcers
  • colitis
  • hardening of the arteries
  • Crohn’s disease
  • dental caries
  • diabetes
  • gum disease which is a major cause of heart attacks or death through C. difficile infections

In return for all of the support, repair, and maintenance that those trillions provide us, they occupy our bodies as their home, and their devotion never wavers until death do us part. Even our brains depend on certain bacteria. In one study it was found that the emotional response of people taking a probiotic-rich fermented milk product greatly differed from the controls, as measured by functional magnetic resonance imaging.

These microbes inhabit both our inner and outer terrains, from the skin (the body’s largest organ) to the body cavities to the deepest recesses of our intestines. At the Human Microbiome Congress in February 2016, the title of one presentation was: “Armpit Microbiome: Why Should We Care?” It turns out that we should care very much – so be sure to avoid that toxic deodorant! According to the experts, human sweat is odourless unless the diversity of the resident microbiome is made deficient by toxins that have the ability to disrupt microbial integrity. Smelly armpits, therefore, are a sign of dysbiosis in the gut, which in turn leaks into the lymphatic system from where the body tries to eliminate toxins through its lymph nodes. (Editor’s note: Thankfully, introduction of healthy bacteria (probiotics) along with bowel detoxification through an organic diet and vitamin C can restore us to socially acceptable levels of odour without chemical deodorants.)

In pregnant women, just prior to giving birth, a specialized team of microbes congregates to await the great event. As the baby progresses through the birth canal towards daylight, this microbial team provides the baby with enzymes which enable the baby to digest breast milk within hours. As humans grow and mature, they benefit from the many evolving and helpful microbes that produce the enzymes needed to make the nutrients in food available for digestion and assimilation.

On the other hand, Leafcutter ants are not as lucky as we are because they don’t carry these helpful microbes inside them as we do: they have to go and create gardens in which they grow a special fungus which creates the enzymes the ants harvest to make those shredded leaves digestible for them. Our intestines already have those gardens – groups of microbes living in biofilms and working as teams on our behalf.

Peer Bork, of the European Microbiome Consortium, discovered that these  trillions fall into three major bacterial ecosystems he calls enterotypes. For example,  Enterotype 1 produces enzymes to make vitamin B7 (biotin) while Enterotype 2 specializes in B1 (thiamine). These enterotypes are not related in any way to gender, ethnicity, or geographic regions. They are like blood types – universal. Therefore, suggests Bork, restoring a person’s diminished enterotype might offer a far better treatment protocol than antibiotics.

New Research Techniques Aid Exploration of the Universe Within

In 2007, the U.S. National Institutes of Health launched the Human Microbiome Project, and at the same time the Metagenomics of the Human Intestinal Tract Project (MetaHIT) and MyNewGut project were launched in Europe and China. All of the research results that came out of those projects have now been published with free access to the public.

On the other hand, the Human Genome Project triggered a huge surprise when it revealed that humans only have 23,000 genes – about the same as a banana; many plants and animals have far more genes than we do. As well, the hope of finding a one-on-one relationship between a gene and a disease was dashed. The fundamental organizing principle in the human genome became even more mysterious.  If our DNA is not the central organizational force, then what is? A lot was known about gut dysbiosis as a serious side effect of antibiotics, but a full appreciation of the hidden universe became only possible when technology evolved  and when a new way of thinking was adopted.

Around 2005, DNA sequencing techniques, originally developed in the 1970s,  made high-throughput sequencing possible, a technique that allows researchers to sequence the DNA of an entire environmental sample. All of a sudden the trillions appeared in view!

Meanwhile, as one of the most influential microbiome researchers, Deborah Goldberg explains, the science of ecology was ready to provide the methodological and computational tools “to compare ‘community structure’ – the diversity, composition, and relative abundance of species of trees in a hectare of forest, or of algae in a litre of lake water, or of bacteria in a gram of soil. These ecological approaches have also been applied to the microbiota of the human mouth, stomach, and skin, and they have been used to compare gastrointestinal microbiota among monozygotic and dizygotic twins and to characterize the community structure of lung bacteria among cystic fibrosis patients. Extending those ecological metrics of community structure to the huge volumes of genomic data from healthy and diseased microbiota [enables understanding] the impact of microorganisms on health.”

Most importantly, ecologists showed medical researchers that the 18th century assumptions about ‘balance of nature’, homeostasis, and the war against disease have to be discarded. Said Goldberg: “A key characteristic of ecological systems – whether tropical forests or human microbiota – is that they are highly variable over time and space. The notion of a ‘balance of nature’, a finely-tuned equilibrium that is static in the absence of anthropogenic disturbance, has long since been discarded in modern ecology.”

Within about five years the whole field exploded with research, much of it with highly successful therapeutic applications. A whole bunch of science journals simultaneously published their first offerings of research results on June 13, 2011.

What Damages Our Microbiome the Most?

In April 2014, the first results of a research project focused on the microbiome of the African Hadza hunter-gatherers was published in the science journal Nature. The Hadza have a microbiome that is so rich and diverse it has almost no parallel within any other culture. Only kids in Italy raised on the Mediterranean Diet, free of GMOs, antibiotics, and pesticide residues came close.  The main finding was that this tremendous diversity in the Hadza microbiome not only protects them against infectious disease, but allows for far more fibre to be made digestible through the help of the microbes residing in their guts, fibre which contains a wide array of nutrients.

North Americans, on the other hand, have been systematically killing off helpful microbial populations ever since the overuse of antibiotics began, especially in agriculture. So it stands to reason that the usual suspects are to blame for our chronic illnesses, including:

  • antibiotics prescribed carelessly and/or incorrectly for a variety of human health problems;
  • wide availability of GMO foods which are nutrient-deficient and toxic to the gut;
  • pesticides which are chemically near-identical to anti-biotics and act as hormone mimics;
  • toxic germicidal household cleaners and laundry soaps;
  • mono-agricultural practices that gives us nutrient- and mineral-deficient food;
  • refined sugars.

All of the items in the above list have been placed on a ‘Not Recommended’ list by most naturopaths, doctors trained by the American Academy for Environmental Medicine, geniuses like Crohn’s Disease expert Elaine Gottschall, and cancer experts like Max Gerson and the late Dr. Nicholas Gonzalez.

Nutrient deficiency as a source of mental illness, a concept which was researched and proven by Dr. Abram Hoffer, and the restoration of health with vitamin C as taught by Linus Pauling, are now not only relevant – they have been validated by the most advanced science in the world.

Furthermore, we now know beyond doubt that just a single course of antibiotics can wipe out our life-supporting gut microbiome for at least a year, as discussed in Carl Zimmer’s excellent 2012 article “When You Swallow a Grenade” (see Resource List at end). And now we also know that the nutrient-devoid junk food served in old age homes and hospitals (which is usually further damaged by microwave ovens), also destroys the consumer’s microbiome. (The studies on this include evidence of serious malnutrition in patients in long-term hospitals and occupants in old age homes.)

So now, when your doctor prescribes a possibly necessary course of antibiotics (think Lyme disease, meningitis, or severe infection), or some dreadful cancer therapy, you can say, “Yes, but what are we going to do about the resulting damage to my gut biome?” And in that question you are backed by the world’s leading scientists whose work is available for free on the internet.

Dawn of a New Medicine

Our invisible universe of microbes keep us in a state of homeodynamics: everything is in flux and no ideal and preordained endpoint of a correctly balanced state of health exists. The biochemical warfare paradigm is cracked beyond repair. The ancient idea of one illness being due to one characteristic cause dissolves into a plethora of potential causes and, therefore, a need for individualized therapeutics. The regulatory bodies in medicine will probably have some choking experiences when their battle for “standards of practice” is overwhelmed by an inescapable diversity of possible approaches.

All of this also renders statistical thinking as obsolete because the individuality of the microbiome rules supreme and requires individualized dialogue, not averaging out of details. Without statistical thinking, which sweeps drug side effects and nutrient depletion caused by pharmaceuticals under the carpet,  Big Pharma’s marketing departments will have to rethink, retool, accept the new reality, or pack it in. The trillions cannot be patented.

We’re going to have to undertake more and more conversations with microbes and do less and less searching for new blockbuster drugs. We must become colleagues with the bugs and trim our big egos. Our lives depend on them.


  • Blaser, M. MD, The Missing Microbes: How Killing Bacteria Creates Modern Plagues, 2014
  • Foxman, B & Goldberg, D. Why the Human Microbiome Project Should Motivate Epidemiologists to Learn Ecology, Epidemiology vol. 21 (6), Nov. 2010
  • The NIH Human Microbiome Project, Genome Research vol. 19, issue 12, Dec. 2009,
  • Mullin, G. E. MD, The Gut Balance Revolution, 2014
  • Drake, D. MD, Vitality article of February 2011 on gut dysbiosis
  • The New York Academy of Sciences. Advances in Human Microbiome Science: Intestinal Diseases. Academy eBriefings. 2015. 2015-eB
  • Structure, function and diversity of the healthy human microbiome, The Human Microbiome Project Consortium, Nature 486, June 14, 2012
  • Shreiner, A. B. et al, The gut microbiome in health and disease, National Institute of Health, Current Opinion in Gastroenter-ology, vol. 31, issue 1, January 2015
  • Morgan, X. C. & Huttenhower, C., Chapter 12: Human Microbiome Analysis, PLoS December 2012 – open access
  • Moya, A., Ferrer, M. Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance. Trends in Microbiology, 2016
  • Schnorr, S. L. et al. Gut microbiome of the Hadza hunter-gatherers. Nature Communications. 5:3654,  2014
  • Zimmer, C.  Bacterial Ecosystems Divide People Into 3 Groups, Scientists Say, The New York Times, April 20, 2011
  • Zimmer, C. When You Swallow A Grenade, posted on Zimmer’s blog The Loom, Dec. 18, 2012
  • Karav, S. et al. Oligosaccharides released from milk glycoproteins are selective growth substrates for infant-associated bifidobacteria, Applied and Environmental Microbiology, 16 April 2016; see News Release: American Society for Microbiology, 13 April 2016
  • Korpela, K. et al,  Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children, Nature Communications, 2016; 7: 10410. PubMed: 26811868.
  • Zimmer, C. Tending the Body’s Microbial Garden, New York Times, June 18, 2012
  • Specter, M., Germs Are Us, The New Yorker, Oct 22, 2012
  • Leach, J.D., Rewild: You’re 99% Microbe – It’s Time You Started Eating Like It,
  • Harmon, K. Bugs Inside: What Happens When the Microbes That Keep Us healthy Disappear? Scientific American, December 16, 2009
  • News Release October 14, 2015: Off-Kilter, Penn study identifies differences in treatment effect on out-of-balance microbiome in Crohn’s Disease, available through
  • Gottschall, E. Breaking the Vicious Cycle, Kirkton Press, 1994. Gottschall died in 2005. Visit her website, her book is readily available. NOTE: the latest edition has an added chapter about autism and its connection to gastrointestinal problems. The Wikipedia entry on Gottschall’s dietary approach is utter nonsense. Ignore.
  • The Wikipedia entries for Human Microbiome Project, Human Microbiota, and Microbiota are very detailed and excellent, especially because of the explanatory diagrams

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