The Silent Microbiome Crisis


Tobias Rees is the William Dawson Chair in the Department of Social Studies of Medicine at McGill University and a director at the Berggruen Institute. Nils Gilman is vice president of programs at the Berggruen Institute.

It is a crisis some scientists believe has similar proportions to climate change, but it gets much less coverage: Microbes are disappearing from our bodies.

You may have heard that trillions of microbes — bacteria, fungi, viruses, protists — live on every surface of your body as well as inside your mouth, other orifices and your gut. You may have also heard that these microbes make up the majority of your body’s cells.

But few are aware of how directly these microbes and their genes affect the functioning of our bodies. The human genome found in the nuclei of our cells contains roughly 20,000 genes, but the microbiome — the sum total of genetic material in the microorganisms that live in and on us — contains as many as 20 million genes, all of which are directly or indirectly interacting with and at times even controlling our genes.

Our microbial genes are critical to the regulation of our metabolism, to the ability of our immune system to fight off infection and to the production of the neurotransmitters that power our brain and nervous system. The microbiome, just like our nuclear genome, is heritable. The majority of microbes are transferred from mother to child during childbirth, in a chain of transmission that reaches back to the earliest animals that evolved — which happen to have been microbes.

So why the crisis?

What we eat

The first major issue is the modern diet. Our hunter-gatherer ancestors mostly ate a plant-based and fiber-rich diet, which sustained a diverse microbial population in our guts that could produce all the metabolites our bodies and brains needed to grow and flourish. By contrast, most modern humans rely on a narrow, nutritionally impoverished and fiber-poor diet. This starves large parts of our microbiome and disrupts our health through typical “diseases of modernity,” such as obesity and diabetes.

The microbial diversity found in the guts of contemporary hunter and gatherer societies, such as the Hadza people in Tanzania or the Yanomami of South America, is roughly twice as high as the one found in the average European and American gut (independent of ethnicity). The good news is that in most cases, if we return to a diverse, fiber-rich diet before essential microbes are lost, some of the diversity of our gut’s microbial population can be restored.

How we are born

Another element of the microbiome crisis is the sharp rise in the number of births via Caesarean section. This form of medical intervention saves the lives of many mothers and babies. But when the procedure is not medically required, it unnecessarily interferes with an important stage of development. Today, a third of the babies born in the U.S., and as many as half of the babies in some countries, such as Brazil and Turkey, are born by C-section.

Why is this a problem? Because traditionally, the initial inoculation of a newborn baby with the mother’s microbiomes happens when a baby travels through the mother’s birth canal. In fact, during the third trimester of pregnancy, a mother’s vaginal and fecal microbiome transforms to inoculate the fetus with essential microbes it needs for optimal development.

A C-section thus disrupts an age-old transmission process, and the effects are real and serious. A child born by C-section is significantly more likely to develop allergies than those who were born naturally, due to an absence of microbes that are critically involved in the development of the immune system.

To make matters more dramatic: since a baby girl born by C-section has permanently lost essential microbes, as an adult she cannot pass these essential microbes on to her own offspring. The situation worsens if her baby is born via C-section and worsens further if the child relies on a low-fiber diet. The compounding exponential effect of all this is obvious.

Each time a mother loses a single microbial species — perhaps one essential for our health — her future children will miss that microbial species too. And if the mother then gets a series of antibiotic treatments, perhaps right before or even during a pregnancy, her children will miss even more essential microbes. Recent research suggests that a newborn who misses just three microbial species during the first three weeks of life is much more likely to be asthmatic.

When we get sick

Still, the rampant use of antibiotics appears to be the single most important disruptor of the human genome-microbiome symbiosis. Dr. Martin Blaser’s book on the matter, “Missing Microbes, may prove to be for antibiotics what Rachel Carson’s “Silent Springwas to the chemical pesticide industry.

Broad-spectrum antibiotics effectively kill many pathogens that make us sick but also kill many microbes that are necessary for normal development. And there is abundant evidence that antibiotics are overused: an average American child gets five courses of broad-spectrum antibiotics during the first three years of life.

Given our mutualistic dependence on microbes, the use of antibiotics to fight infections is like using saturation bombing to deal with an insurgency. It’s a crude function that produces huge amounts of collateral damage to the “good” microbiome. At worst, especially if not pursued to conclusion, the antibiotic may not only fail to kill off the underlying infection but may strengthen the insurgency, which results in antibiotic resistance. As with poorly designed counterinsurgency strategies, the indiscriminate use of antibiotics can have devastating unintended consequences.

One such unintended consequence happens because the majority of antibiotics are used not in humans but in farm animals. Several thousand metric tons a year are fed to livestock and sprayed on fields at a subtherapeutic level. This is not so much to prevent disease but to increase weight gain (or, to put it differently, obesity) in animals, thus increasing meat production. Then we consume these animals’ antibiotic-drenched flesh. The animals also transfer antibiotics into the groundwater, which we eventually drink. All of this helps destroy our own microbiome.

The introduction of mass antibiotics coincides with the dramatic increase of a whole series of modern plagues, all of which have experimentally been linked to microbiome disturbances: atopic diseases, autoimmune diseases, allergies, asthma, even multiple sclerosis and Parkinson’s disease. Scientists are now also exploring links between the disturbance of microbes and some cancers.

Where we go from here

As individuals, we can respond to this epidemic by changing what we eat and also by getting close to nature: when we work in our gardens and get our hands dirty, our bodies soak up healthy microbes or microbial metabolites.

For policymakers, this emerging understanding of the importance of the human microbiome provides even more reason to crack down on the rampant over-prescription of antibiotics. Policymakers should also be funding more research into both the complex interactions between the human microbiome, various animal microbiomes, diet, environmental factors and personal and public health practices.

In addition, scientists need to build biobanks: just like we have seed vaults for plants at risk of extinction, we need to collect microbiome samples from populations that don’t live a modern lifestyle and who have a much richer, more diverse microbiome than we do. Regenerative microbe therapies and microbial transplants are rapidly emerging as important medical interventions, and many scientists think this is a vital step for the future of medicine.

Finally, and perhaps most profoundly, the lesson of the human microbiome is that it compels us to revise our understanding of ourselves as humans: Microbes are us. In fact, it is impossible to clearly determine where a human being ends and its microbiome begins: there is a quintessential indistinguishability. We humans are not more than mere nature. In fact, we are just that — a piece of nature, deeply interrelated with the microbial environment on which we are utterly contingent.

This was produced by The WorldPost, a partnership of the Berggruen Institute and The Washington Post.