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We Kill Germs at Our Peril

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‘Missing Microbes’: How Antibiotics Can Do Harm


Missing Microbes
How the Overuse of Antibiotics Is Fueling Our Modern Plagues. By Martin J. Blaser, M.D. Henry Holt and Company. 273 pages. $28.



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You never get something for nothing, especially not in health care. Every test, every incision, every little pill brings benefits and risks.

Nowhere is that balance tilting more ominously in the wrong direction than in the once halcyon realm of infectious diseases, that big success story of the 20th century. We have had antibiotics since the mid-1940s — just about as long as we have had the atomic bomb, as Dr. Martin J. Blaser points out — and our big mistake was failing long ago to appreciate the parallels between the two.

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Antibiotics have cowed many of our old bacterial enemies into submission: We aimed to blast them off the planet, and we dosed accordingly. Now we are beginning to reap the consequences. It turns out that not all germs are bad — and even some bad germs are not all bad. In “Missing Microbes,” Dr. Blaser, a professor at the New York University School of Medicine, presents the daunting array of reasons we have to rethink the enthusiastic destruction of years past.


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First and foremost, the war has escalated. Imprudent antibiotic use has resulted in widespread resistance among microbes; infectious disease doctors (I am one, as well as a casual acquaintance of Dr. Blaser’s) now operate in a state of permanent near panic as common infections demand increasingly powerful drugs for control.

Second, as always, it is the hapless bystanders who have suffered the most — not human beings, mind you, but the gazillions of benevolent, hardworking bacteria colonizing our skin and the inner linings of our gastrointestinal tracts. We need these good little creatures to survive, but even a short course of antibiotics can destroy their universe, with incalculable casualties and a devastated landscape. Sometimes neither the citizenry nor the habitat ever recovers.

And finally, there is the accumulation of disheartening evidence that the war against the old plagues is simply leading to worse wars against a whole series of new ones.

Parts of Dr. Blaser’s argument are familiar, such as the story of Clostridium difficile colitis, an increasingly common cause of diarrhea. This condition arises most often when a course of antibiotics skews the normal microbial population of the gut to favor a single toxin-producing organism. Sometimes yet more antibiotics will restore normal intestinal function. But sometimes no treatment works — nothing but infusing feces full of normal bacteria into the ailing intestines, a last-ditch strategy that has proved stunningly successful. Without it, otherwise perfectly healthy people can die.

Less familiar is the paradox posed by the little comma-shaped organism Helicobacter pylori, a denizen of the human stomach. Dr. Blaser is one of the world’s experts in these “ulcer bacteria,” which are associated not just with ulcers but also with stomach cancer. We have been slowly eradicating H. pylori with antibiotics — the organisms have become quite uncommon in developed countries.

But as they vanish, Dr. Blaser notes, a small epidemic of esophageal disease follows, with inflammation causing heartburn and even cancer. It turns out that this bad germ is also good, instrumental in protecting the human esophagus from trouble.

And that’s not all, folks, far from it.

We know that giving antibiotics to young chickens, cows and pigs means bigger, fatter animals brought to market. But we are doing pretty much the same thing to our own young, repeatedly dosing them up against all the infections of childhood (many of which do not require antibiotics to resolve). The results of an interconnected series of experiments in Dr. Blaser’s lab, with infant mice fed a variety of antibiotic regimens, lend strong support to the theory that exposure to antibiotics early in life has long-term effects on metabolism, and may contribute to our epidemic of childhood and adult obesity.

For other increasingly common conditions such as asthma, inflammatory bowel disease and celiac disease, Dr. Blaser offers an inversion of the so-called hygiene hypothesis, which holds that by removing us from contact with outdoor microbes, sanitized modern life has allowed the immune system to spiral out of control. Instead, he suggests, blame rests on the distortion of our internal microbial world.

Antibiotics are partly responsible, but so are other medical habits, such as our increasing use of cesarean sections. These aseptic procedures prevent newborns from acquiring their mothers’ organisms through the birth canal, possibly setting them up for a lifetime of trouble, with higher than normal risks of a range of immune-related problems.

Dr. Blaser presents this all at a rapid clip, not stinting on the technical language but infusing enough human interest to make his argument and data reasonably accessible. (He had writing help from Sandra Blakeslee, a veteran science journalist and a frequent contributor to Science Times.)

The discerning reader should not forget that the research he discusses is largely his own; we hear no dissenting voices or contradictory evidence, although much of the narrative remains scientifically hypothetical.

That said, however, the weight of evidence behind Dr. Blaser’s cautions about antibiotics is overwhelming. They are certainly lifesaving drugs — they saved his own life when he had typhoid fever, and he testified in Congress recently on the urgent need to develop better and stronger ones. But they are also immensely dangerous, both to individuals and to the firmly linked communities of microbes and men.

Correction: May 1, 2014

Because of an editing error, a review on Tuesday about the book “Missing Microbes” misidentified a condition that the author, Dr. Martin J. Blaser, argues is caused by an imbalance of internal microbes. It is inflammatory bowel disease, not inflammatory bowel syndrome.

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