Missing Microbes

How Killing Bacteria Creates Modern Plagues

Martin Blaser

• Publisher: Oneworld Publications
• Year: 2014
• eBook ISBN: 9781780744421
• Topic: Biological Sciences
• Subtopic: Science General
• Index: Biological Sciences

A clarion call to save humanity’s most essential fellow creatures – and our health

Far beneath our skin exists an unfathomable, ancient universe – an internal ecosystem that is critical to our health. Dr Martin Blaser invites us into the wilds of the human ‘microbiome’, unfurling its inner workings and evolution. For thousands of years, bacteria and human cells have co-existed in a relationship that has ensured the health and equilibrium of our body. But now, much like the natural world outside of us, our internal environment is being irrevocably destroyed. The culprit: some of our most revered medical advances – antibiotics – which appear to be linked to the epidemics of asthma, eczema, obesity, certain forms of cancer, and other diseases plaguing modern society.

In a book that stands as the Silent Spring of its day, Blaser sounds a provocative alarm that we ignore at our peril.

1.

MODERN PLAGUES

I never knew two of my father’s sisters. In the little town where they were born, early in the last century, they didn’t see their second birthdays. They had high fevers, and I am not sure what else. The situation was so dire that my grandfather went to the prayer house and changed his daughters’ names to fool the angel of death. He did this for each girl. It did no good.

In 1850, as many as four in ten English babies died before his or her first birthday. Lethal epidemics swept through crowded cities, as people were packed into dark, dirty rooms with fetid air and no running water. Familiar scourges included cholera, pneumonia, scarlet fever, diphtheria, whooping cough, tuberculosis, and smallpox.

Today, fewer than five in every thousand infants in the United Kingdom are expected to die before age one—a remarkable improvement. Over the past century and a half, the nation as well as other countries in the developed world have been getting healthier. Chalk it up to improved sanitation, rat control, clean drinking water, pasteurized milk, childhood vaccinations, modern medical procedures including anaesthesia, and, of course, nearly seventy years of antibiotics.

In today’s world, children grow up without the deformed bones caused by lack of vitamin D or ‘cloudy’ sinuses from infections. Nearly all women survive childbirth. Eighty-year-olds, once consigned to the veranda, are swatting tennis balls, often with the help of a metal hip joint.

Yet recently, just within the past few decades, amid all of these medical advances, something has gone terribly wrong. In many different ways we appear to be getting sicker. You can see the headlines every day. We are suffering from a mysterious array of what I call ‘modern plagues’: obesity, childhood diabetes, asthma, hay fever, food allergies, oesophageal reflux and cancer, coeliac disease, Crohn’s disease, ulcerative colitis, autism, eczema. In all likelihood you or someone in your family or someone you know is afflicted. Unlike most lethal plagues of the past that struck relatively fast and hard, these are chronic conditions that diminish and degrade their victims’ quality of life for decades.

The most visible of these plagues is obesity, defined in terms of the body mass index (BMI), which expresses the relationship between a person’s height and weight. People of healthy weight have a BMI between 20 and 25. Those whose BMI is between 25 and 30 are overweight. Everyone with a BMI over 30 is obese. Barack Obama has a BMI of about 23. David Cameron sits somewhere between 25 and 30. Winston Churchill, who weighed eighteen stone and stood five feet eight inches tall, had a BMI of 38.

Britain is the fattest nation in Western Europe, with more than a quarter of the population ranked as obese. The U.K. rate of 26.1 is more than twice that in France, at 12.9 percent. Next time you go to an airport terminal or supermarket, look around and see for yourself. The obesity epidemic is not just a British problem; it’s global. As of 2008, according to the World Health Organization (WHO), 1.5 billion adults were overweight; of these, over 200 million men and nearly 300 million women qualified as obese. Many of these people live in developing countries associated more with famine than with overeating.

These figures are alarming, but the really shocking fact is that this accumulation of global human body fat has been accelerating not over the course of a few centuries but in a mere two decades. Yet fat- and sugar-rich foods, so often blamed for all the extra pounds, have been ubiquitous for a good deal longer than that, at least in the developed world, and the new generations of overweight people in the third world have not suddenly adopted a deep-fried-fish-and-chips pub-style diet. Epidemiologic studies have shown that high caloric intake, while definitely not helpful, is not sufficient to explain the distribution or course of the worldwide obesity epidemic.

At the same time, the autoimmune form of diabetes that begins in childhood and requires insulin injections (juvenile or Type 1 diabetes) has been doubling in incidence about every twenty years across the industrialized world. In Finland, where record keeping is meticulous, the incidence has risen 550 percent since 1950. This increase is not because we are detecting Type 1 diabetes more readily. Before insulin was discovered in the 1920s, the disease was always fatal. Nowadays, with adequate treatment, most children survive. But the disease itself has not changed; something in us has changed. Type 1 diabetes is also striking younger children. The average age of diagnosis used to be about nine. Now it is around six, and some children are becoming diabetic when they are three.

The recent rise in asthma, a chronic inflammation of the airways, is similarly alarming. There are 5.4 million people with asthma in the United Kingdom, affecting one in five households. One in every eleven children suffers wheezing, breathlessness, chest tightness, and coughing. The rate of childhood asthma increased by 50 percent from 2001 through 2009 in the United States, and the rise has not spared any ethnicity; the rates were initially different in various groups, but all have been rising.

Asthma is often triggered by something in the environment such as tobacco smoke, mould, air pollution, cockroach leavings, colds, and flu. Once an attack begins, asthmatics gasp for air and, without quick medication, are rushed to an accident and emergency room. Even with the best care, they can die, as did the son of a physician colleague. No economic or social class has been spared.

Food allergies are everywhere. A generation ago, peanut allergies were extremely rare. Now, if you stroll through any preschool, you will see walls plastered with ‘nut-free zone’ bulletins. More and more children suffer immune responses to proteins in foods, not just in nuts but in milk, eggs, soy, fish, fruits—you name it, someone is allergic to it. Coeliac disease, an allergy to gluten, the main protein in wheat flour, is rampant. More than a third of British teenagers suffer from hay fever. Eczema, a chronic skin inflammation, affects more than 15 percent of children in the United States. In industrialized nations, the number of kids with eczema has tripled in the past thirty years.

These disorders suggest that our children are experiencing levels of immune dysfunction never seen before, as well as conditions such as autism, a much discussed and debated modern plague that is a focus of my laboratory. Nor are adults escaping their own share of modern plagues. The incidence of inflammatory bowel disease, including Crohn’s and ulcerative colitis, is rising, wherever we look.

When I was a medical student, oesophageal reflux, which causes heartburn, was uncommon. But the ailment has exploded in these past forty years, and the cancer it leads to, adenocarcinoma of the oesophagus, is the most rapidly increasing cancer in the United Kingdom and everywhere else it has been tracked, and is a particularly nasty problem for Caucasian men.

Why are all of these maladies rapidly rising at the same time across the developed world and spilling over into the developing world as it becomes more Westernized? Can it be a mere coincidence? If there are ten of these modern plagues, are there ten separate causes? That seems unlikely.

Or could there be one underlying cause fuelling all these parallel increases? A single cause is easier to grasp; it is simpler, more parsimonious. But what cause could be grand enough to encompass asthma, obesity, oesophageal reflux, juvenile diabetes, and allergies to specific foods, among all of the others? Eating too many calories could explain obesity but not asthma; many of the children who suffer from asthma are slim. Air pollution could explain asthma but not food allergies.

Many theories have been proposed to explain each disorder: lack of sleep makes you fat; vaccines lead to autism; genetically engineered wheat strains are toxic to the human gut; and so on.

The most popular explanation for the rise in childhood illness is the so-called hygiene hypothesis. The idea is that modern plagues are happening because we have made our world too clean. The result is that our children’s immune systems have become quiescent and are therefore prone to false alarms and friendly fire. A lot of parents these days try to ramp up their children’s immune systems by exposing them to pets, farm animals, and barnyards or better still by allowing them to eat dirt.

I beg to differ. To me, such exposures are largely irrelevant to our health. The microbes present in dirt have evolved for soil, not for us. The microbes in our pets and farm animals also are not deeply rooted in our human evolution. The hygiene hypothesis, as I will show you, has been misinterpreted.

Rather we need to look closely at the microorganisms that make a living in and on our bodies, massive assemblages of competing and cooperating microbes known collectively as the microbiome. In ecology, biome refers to the sets of plants and animals in a community such as a jungle, forest, or coral reef. An enormous diversity of species, large and small, interact to form complex webs of mutual support. When a keystone species (think wolves in Scotland) disappears or goes extinct the ecology suffers. It can even collapse.

Each of us hosts a similarly diverse ecology of microbes that has coevolved with our species over millennia. They thrive in the mouth, gut, nasal passages, ear canal, and on the skin. In women, they coat the vagina. The microbes that constitute your microbiome are generally acquired early in life; surprisingly, by the age of three, the populations within children resemble those of adults. Together, they play a critical role in your immunity as well as your ability to combat disease. In short, it is your microbiome that keeps you healthy. And parts of it are disappearing.

The reasons for this disaster are all around you, including overuse of antibiotics in humans and animals, Caesarian sections, and the widespread use of sanitizers and antiseptics, to name just a few. While antibiotic resistance is a huge problem—old killers like tuberculosis are increasingly resistant and making a comeback—there now seem to be separate ones, affecting people with such scourges as Clostridium difficile (C. diff), bacteria of the digestive tract resistant to multiple antibiotics, a potential danger in hospital, and a spreading pathogen, methicillin-resistant Staphylococcus aureus (MRSA), which can be acquired anywhere. The selective pressure of antibiotic use is clearly increasing their presence.

But as terrible as these resistant pathogens are, the loss of diversity within our microbiome is far more pernicious. Its loss changes development itself, affecting our metabolism, immunity, and cognition.

I have called this process the ‘disappearing microbiota’. It’s a funny term that does not immediately roll off your tongue, but I believe it is correct. For a number of reasons, we are losing our ancient microbes. This quandary is the central theme of this book. The loss of microbial diversity on and within our bodies is exacting a terrible price. I predict it will be worse in the future. Just as the internal combustion engine, the splitting of the atom, and pesticides all have had unanticipated effects, so too does the abuse of antibiotics and other medical or quasi-medical practices (e.g., sanitizer use).

An even worse scenario is headed our way if we don’t change our behaviour. It is one so bleak, like a blizzard roaring over a frozen landscape, that I call it ‘antibiotic winter’. I don’t want the babies of the future to end up like my poor aunts. That is why I am sounding an alarm.

My personal journey towards the realization that our friendly microbes are in trouble began on 9 July 1977. I remember the date because it was the first time I heard the name of a microbe, Campylobacter, that literally set my life’s research into motion. I was a newly minted fellow in infectious diseases at the University of Colorado Medical Center in Denver.

That morning I was asked to see a thirty-three-year-old patient who had come to the hospital a few days earlier. He had been suffering from a high fever and was confused. A spinal tap confirmed that he had meningitis, a serious inflammation of the nervous system. His doctors sent samples of his blood and spinal fluid to the culture lab to determine whether the cause was a bacterial infection and, if so, to find out what kind of bacterium it was. While those tests were pending, they started him on antibiotics anyway because he looked quite ill. They believed that he needed big doses of antibiotics immediately or he would die. They were correct.

The test results revealed a slow-growing bacterium identified as Campylobacter fetus, an organism that no one at the hospital had ever heard of. That’s why I was called. On the job for nine whole days, I was supposed to know the answers.

Campylobacter organisms are a genus of spiral-shaped bacteria. Like that of so many tiny corkscrews, their helical shape helps them penetrate the gelatin-like mucus that lines the gastrointestinal tract. But why the odd species name fetus? (In biology, each organism is identified first by the name of its genus, in this case Campylobacter, and then by its species, in this case fetus. Each genus has many species and subspecies. Humans are Homo sapiens: of the genus Homo and the species sapiens.) Digging into the medical literature, I discovered that the microbe had this strange name because it affected pregnant sheep and cattle, causing them to abort. It rarely infected humans. How our patient got infected was a mystery. He was a city man, a musician.

Once we knew the organism, we tailored an appropriate antibiotic treatment, and the patient recovered in a couple of weeks. Meanwhile, I was scheduled to give a talk at a clinical conference and decided I would speak about Campylobacter. What could be better than talking about a rare infection that no one knew anything about? My own ignoran...

Table of contents

• Cover
• Title
• Epigraph
• Contents
• 1. Modern Plagues
• 2. Our Microbial Planet
• 3. The Human Microbiome
• 4. The Rise of Pathogens
• 5. The Wonder Drugs
• 6. The Overuse of Antibiotics
• 7. The Modern Farmer
• 8. Mother and Child
• 9. A Forgotten World
• 10. Heartburn
• 11. Trouble Breathing
• 12. Taller
• 13. . . . and Fatter
• 14. Modern Plagues Revisited
• 15. Antibiotic Winter
• 16. Solutions
• Epilogue
• Notes
• Acknowledgements
• Index
• About the Author
• Copyright