So why, you are bound to ask at some point in your life, do microbes so often want to hurt us? What possible satisfaction could there be to a microbe in having us grow feverish or chilled, or disfigured with sores, or above all expire? A dead host, after all, is hardly going to provide long-term hospitality.

To begin with, it is worth remembering that most microorganisms are neutral or even beneficial to human well-being. The most rampantly infectious organism on Earth, a bacterium called Wolbachia, doesn’t hurt humans at all—or, come to that, any other vertebrates—but if you are a shrimp or worm or fruit fly, it can make you wish you had never been born. Altogether, only about one microbe in a thousand is a pathogen for humans, according toNational Geographic —though, knowing what some of them can do, we could be forgiven for thinking that that is quite enough. Even if mostly benign, microbes are still the number-three killer in the Western world, and even many less lethal ones of course make us deeply rue their existence.

Making a host unwell has certain benefits for the microbe. The symptoms of an illness often help to spread the disease. Vomiting, sneezing, and diarrhea are excellent methods of getting out of one host and into position for another. The most effective strategy of all is to enlist the help of a mobile third party. Infectious organisms love mosquitoes because the mosquito’s sting delivers them directly to a bloodstream where they can get straight to work before the victim’s defense mechanisms can figure out what’s hit them. This is why so many grade-A diseases—malaria, yellow fever, dengue fever, encephalitis, and a hundred or so other less celebrated but often rapacious maladies—begin with a mosquito bite. It is a fortunate fluke for us that HIV, the AIDS agent, isn’t among them—at least not yet. Any HIV the mosquito sucks up on its travels is dissolved by the mosquito’s own metabolism. When the day comes that the virus mutates its way around this, we may be in real trouble.

It is a mistake, however, to consider the matter too carefully from the position of logic because microorganisms clearly are not calculating entities. They don’t care what they do to you any more than you care what distress you cause when you slaughter them by the millions with a soapy shower or a swipe of deodorant. The only time your continuing well-being is of consequence to a pathogen is when it kills you too well. If they eliminate you before they can move on, then they may well die out themselves. This in fact sometimes happens. History, Jared Diamond notes, is full of diseases that “once caused terrifying epidemics and then disappeared as mysteriously as they had come.” He cites the robust but mercifully transient English sweating sickness, which raged from 1485 to 1552, killing tens of thousands as it went, before burning itself out. Too much efficiency is not a good thing for any infectious organism.

A great deal of sickness arises not because of what the organism has done to you but what your body is trying to do to the organism. In its quest to rid the body of pathogens, the immune system sometimes destroys cells or damages critical tissues, so often when you are unwell what you are feeling is not the pathogens but your own immune responses. Anyway, getting sick is a sensible response to infection. Sick people retire to their beds and thus are less of a threat to the wider community. Resting also frees more of the body’s resources to attend to the infection.

Because there are so many things out there with the potential to hurt you, your body holds lots of different varieties of defensive white cells—some ten million types in all, each designed to identify and destroy a particular sort of invader. It would be impossibly inefficient to maintain ten million separate standing armies, so each variety of white cell keeps only a few scouts on active duty. When an infectious agent—what’s known as an antigen—invades, relevant scouts identify the attacker and put out a call for reinforcements of the right type. While your body is manufacturing these forces, you are likely to feel wretched. The onset of recovery begins when the troops finally swing into action.

White cells are merciless and will hunt down and kill every last pathogen they can find. To avoid extinction, attackers have evolved two elemental strategies. Either they strike quickly and move on to a new host, as with common infectious illnesses like flu, or they disguise themselves so that the white cells fail to spot them, as with HIV, the virus responsible for AIDS, which can sit harmlessly and unnoticed in the nuclei of cells for years before springing into action.

One of the odder aspects of infection is that microbes that normally do no harm at all sometimes get into the wrong parts of the body and “go kind of crazy,” in the words of Dr. Bryan Marsh, an infectious diseases specialist at Dartmouth–Hitchcock Medical Center in Lebanon, New Hamphire. “It happens all the time with car accidents when people suffer internal injuries. Microbes that are normally benign in the gut get into other parts of the body—the bloodstream, for instance—and cause terrible havoc.”

The scariest, most out-of-control bacterial disorder of the moment is a disease callednecrotizing fasciitis in which bacteria essentially eat the victim from the inside out, devouring internal tissue and leaving behind a pulpy, noxious residue. Patients often come in with comparatively mild complaints—a skin rash and fever typically—but then dramatically deteriorate. When they are opened up it is often found that they are simply being consumed. The only treatment is what is known as “radical excisional surgery”—cutting out every bit of infected area. Seventy percent of victims die; many of the rest are left terribly disfigured. The source of the infection is a mundane family of bacteria called Group A Streptococcus, which normally do no more than cause strep throat. Very occasionally, for reasons unknown, some of these bacteria get through the lining of the throat and into the body proper, where they wreak the most devastating havoc. They are completely resistant to antibiotics. About a thousand cases a year occur in the United States, and no one can say that it won’t get worse.

Precisely the same thing happens with meningitis. At least 10 percent of young adults, and perhaps 30 percent of teenagers, carry the deadly meningococcal bacterium, but it lives quite harmlessly in the throat. Just occasionally—in about one young person in a hundred thousand—it gets into the bloodstream and makes them very ill indeed. In the worst cases, death can come in twelve hours. That’s shockingly quick. “You can have a person who’s in perfect health at breakfast and dead by evening,” says Marsh.

We would have much more success with bacteria if we weren’t so profligate with our best weapon against them: antibiotics. Remarkably, by one estimate some 70 percent of the antibiotics used in the developed world are given to farm animals, often routinely in stock feed, simply to promote growth or as a precaution against infection. Such applications give bacteria every opportunity to evolve a resistance to them. It is an opportunity that they have enthusiastically seized.

In 1952, penicillin was fully effective against all strains of staphylococcus bacteria, to such an extent that by the early 1960s the U.S. surgeon general, William Stewart, felt confident enough to declare: “The time has come to close the book on infectious diseases. We have basically wiped out infection in the United States.” Even as he spoke, however, some 90 percent of those strains were in the process of developing immunity to penicillin. Soon one of these new strains, called Methicillin-Resistant Staphylococcus Aureus, began to show up in hospitals. Only one type of antibiotic, vancomycin, remained effective against it, but in 1997 a hospital in Tokyo reported the appearance of a strain that could resist even that. Within months it had spread to six other Japanese hospitals. All over, the microbes are beginning to win the war again: in U.S. hospitals alone, some fourteen thousand people a year die from infections they pick up there. As James Surowiecki has noted, given a choice between developing antibiotics that people will take every day for two weeks or antidepressants that people will take every day forever, drug companies not surprisingly opt for the latter. Although a few antibiotics have been toughened up a bit, the pharmaceutical industry hasn’t given us an entirely new antibiotic since the 1970s.

Our carelessness is all the more alarming since the discovery that many other ailments may be bacterial in origin. The process of discovery began in 1983 when Barry Marshall, a doctor in Perth, Western Australia, found that many stomach cancers and most stomach ulcers are caused by a bacterium calledHelicobacter pylori . Even though his findings were easily tested, the notion was so radical that more than a decade would pass before they were generally accepted. America’s National Institutes of Health, for instance, didn’t officially endorse the idea until 1994. “Hundreds, even thousands of people must have died from ulcers who wouldn’t have,” Marshall told a reporter fromForbes in 1999.

Since then further research has shown that there is or may well be a bacterial component in all kinds of other disorders—heart disease, asthma, arthritis, multiple sclerosis, several types of mental disorders, many cancers, even, it has been suggested (inScienceno less), obesity. The day may not be far off when we desperately require an effective antibiotic and haven’t got one to call on.

It may come as a slight comfort to know that bacteria can themselves get sick. They are sometimes infected by bacteriophages (or simply phages), a type of virus. A virus is a strange and unlovely entity—“a piece of nucleic acid surrounded by bad news” in the memorable phrase of the Nobel laureate Peter Medawar. Smaller and simpler than bacteria, viruses aren’t themselves alive. In isolation they are inert and harmless. But introduce them into a suitable host and they burst into busyness—into life. About five thousand types of virus are known, and between them they afflict us with many hundreds of diseases, ranging from the flu and common cold to those that are most invidious to human well-being: smallpox, rabies, yellow fever, ebola, polio, and the human immunodeficiency virus, the source of AIDS.

Viruses prosper by hijacking the genetic material of a living cell and using it to produce more virus. They reproduce in a fanatical manner, then burst out in search of more cells to invade. Not being living organisms themselves, they can afford to be very simple. Many, including HIV, have ten genes or fewer, whereas even the simplest bacteria require several thousand. They are also very tiny, much too small to be seen with a conventional microscope. It wasn’t until 1943 and the invention of the electron microscope that science got its first look at them. But they can do immense damage. Smallpox in the twentieth century alone killed an estimated 300 million people.

They also have an unnerving capacity to burst upon the world in some new and startling form and then to vanish again as quickly as they came. In 1916, in one such case, people in Europe and America began to come down with a strange sleeping sickness, which became known as encephalitis lethargica. Victims would go to sleep and not wake up. They could be roused without great difficulty to take food or go to the lavatory, and would answer questions sensibly—they knew who and where they were—though their manner was always apathetic.

However, the moment they were permitted to rest, they would sink at once back into deepest slumber and remain in that state for as long as they were left. Some went on in this manner for months before dying. A very few survived and regained consciousness but not their former liveliness. They existed in a state of profound apathy, “like extinct volcanoes,” in the words of one doctor. In ten years the disease killed some five million people and then quietly went away. It didn’t get much lasting attention because in the meantime an even worse epidemic—indeed, the worst in history—swept across the world.

It is sometimes called the Great Swine Flu epidemic and sometimes the Great Spanish Flu epidemic, but in either case it was ferocious. World War I killed twenty-one million people in four years; swine flu did the same in its first four months. Almost 80 percent of American casualties in the First World War came not from enemy fire, but from flu. In some units the mortality rate was as high as 80 percent.

Swine flu arose as a normal, nonlethal flu in the spring of 1918, but somehow over the following months—no one knows how or where—it mutated into something more severe. A fifth of victims suffered only mild symptoms, but the rest became gravely ill and often died. Some succumbed within hours; others held on for a few days.

In the United States, the first deaths were recorded among sailors in Boston in late August 1918, but the epidemic quickly spread to all parts of the country. Schools closed, public entertainments were shut down, people everywhere wore masks. It did little good. Between the autumn of 1918 and spring of the following year, 548,452 people died of the flu in America. The toll in Britain was 220,000, with similar numbers dead in France and Germany. No one knows the global toll, as records in the Third World were often poor, but it was not less than 20 million and probably more like 50 million. Some estimates have put the global total as high as 100 million.

In an attempt to devise a vaccine, medical authorities conducted tests on volunteers at a military prison on Deer Island in Boston Harbor. The prisoners were promised pardons if they survived a battery of tests. These tests were rigorous to say the least. First the subjects were injected with infected lung tissue taken from the dead and then sprayed in the eyes, nose, and mouth with infectious aerosols. If they still failed to succumb, they had their throats swabbed with discharges taken from the sick and dying. If all else failed, they were required to sit open-mouthed while a gravely ill victim was helped to cough into their faces.

Out of—somewhat amazingly—three hundred men who volunteered, the doctors chose sixty-two for the tests. None contracted the flu—not one. The only person who did grow ill was the ward doctor, who swiftly died. The probable explanation for this is that the epidemic had passed through the prison a few weeks earlier and the volunteers, all of whom had survived that visitation, had a natural immunity.

Much about the 1918 flu is understood poorly or not at all. One mystery is how it erupted suddenly, all over, in places separated by oceans, mountain ranges, and other earthly impediments. A virus can survive for no more than a few hours outside a host body, so how could it appear in Madrid, Bombay, and Philadelphia all in the same week?

The probable answer is that it was incubated and spread by people who had only slight symptoms or none at all. Even in normal outbreaks, about 10 percent of people have the flu but are unaware of it because they experience no ill effects. And because they remain in circulation they tend to be the great spreaders of the disease.

That would account for the 1918 outbreak’s widespread distribution, but it still doesn’t explain how it managed to lay low for several months before erupting so explosively at more or less the same time all over. Even more mysterious is that it was primarily devastating to people in the prime of life. Flu normally is hardest on infants and the elderly, but in the 1918 outbreak deaths were overwhelmingly among people in their twenties and thirties. Older people may have benefited from resistance gained from an earlier exposure to the same strain, but why the very young were similarly spared is unknown. The greatest mystery of all is why the 1918 flu was so ferociously deadly when most flus are not. We still have no idea.

From time to time certain strains of virus return. A disagreeable Russian virus known as H1N1 caused severe outbreaks over wide areas in 1933, then again in the 1950s, and yet again in the 1970s. Where it went in the meantime each time is uncertain. One suggestion is that viruses hide out unnoticed in populations of wild animals before trying their hand at a new generation of humans. No one can rule out the possibility that the Great Swine Flu epidemic might once again rear its head.

And if it doesn’t, others well might. New and frightening viruses crop up all the time. Ebola, Lassa, and Marburg fevers all have tended to flare up and die down again, but no one can say that they aren’t quietly mutating away somewhere, or simply awaiting the right opportunity to burst forth in a catastrophic manner. It is now apparent that AIDS has been among us much longer than anyone originally suspected. Researchers at the Manchester Royal Infirmary in England discovered that a sailor who had died of mysterious, untreatable causes in 1959 in fact had AIDS. But for whatever reasons the disease remained generally quiescent for another twenty years.

The miracle is that other such diseases haven’t gone rampant. Lassa fever, which wasn’t first detected until 1969, in West Africa, is extremely virulent and little understood. In 1969, a doctor at a Yale University lab in New Haven, Connecticut, who was studying Lassa fever came down with it. He survived, but, more alarmingly, a technician in a nearby lab, with no direct exposure, also contracted the disease and died.

Happily the outbreak stopped there, but we can’t count on such good fortune always. Our lifestyles invite epidemics. Air travel makes it possible to spread infectious agents across the planet with amazing ease. An ebola virus could begin the day in, say, Benin, and finish it in New York or Hamburg or Nairobi, or all three. It means also that medical authorities increasingly need to be acquainted with pretty much every malady that exists everywhere, but of course they are not. In 1990, a Nigerian living in Chicago was exposed to Lassa fever on a visit to his homeland, but didn’t develop symptoms until he had returned to the United States. He died in a Chicago hospital without diagnosis and without anyone taking any special precautions in treating him, unaware that he had one of the most lethal and infectious diseases on the planet. Miraculously, no one else was infected. We may not be so lucky next time.

And on that sobering note, it’s time to return to the world of the visibly living.