Early in the twentieth century, Dr. Eli Metchnikoff popularized the theory that disease begins in the digestive tract because of an imbalance of intestinal bacteria. He called this state dysbiosis, which comes from symbiosis, meaning “living together in mutual harmony,” and dys-, which means “not.”

Dr. Metchnikoff was the first scientist to discover the useful properties of probiotics. He won the Nobel Prize in 1908 for his work on lactobacilli and their role in immunity and was a colleague of Louis Pasteur, succeeding him as the director of the Pasteur Institute in Paris.

Dr. Metchnikoff found that the bacteria in yogurt prevented and reversed bacterial infection. (He named it Lactobacillus bulgaricus after the long-lived, yogurt-loving peasants of Bulgaria.) His research proved that lactobacilli could displace many diseaseproducing organisms and reduce the toxins they generated.

He believed these endotoxins (toxins produced from substances inside the body) shortened lifespan. He advocated use of lactobacillus in the 1940s for ptomaine poisoning, a widely used therapy in Europe. In more recent decades, Metchnikoff ’s work has taken a backseat to modern therapies, such as antibiotics and immunization programs, which scientists hoped would conquer infectious diseases.

For instance, because of an aggressive worldwide immunization program, the World Health Assembly formally declared on May 8, 1980, that smallpox had been eradicated worldwide, which was an enormous triumph for science and humankind. But, subsequent efforts at eradicating other diseases have been unsuccessful.

While parents in America routinely immunize their children against measles, mumps, and polio, parents in poor nations are coping with the loss of half their children by age ten. Worldwide, we are finding an increase in new and deadly viruses for which there are not yet effective vaccines.

Viruses and bacteria are extremely adaptable, and their success ensures their survival. In our efforts to eradicate them we have pushed them to evolve. Long before chemists created antibiotics, yeasts, fungi, and rival bacteria were producing antibiotics to ward each other off and establish neighborhoods.

They became adept at evading each other’s strategies and adapting for survival. Because people have used antibiotics prophylactically and indiscriminately in humans and animals, the bacteria have had a chance to learn from it, undergoing rapid mutations.

As they shuffle their components, learning new evolutionary dance steps, superstrains of bacteria have been created that no longer respond to any antibiotic treatment. For instance, our immune systems normally detect bacteria by information coded on the cell walls.

Now, in response to antibiotics, some bacteria have survived by removing their cell walls, so they’re able to enter the bloodstream and tissues unopposed, causing damage in organs and tissues. Bacteria can also turn on specific genes when exposed to specific antibiotics.

Resistant strains of bacteria are communicating with each other and passing resistance information on to other types of bacteria. For example, we now have antibiotic-resistant gonorrhea, leprosy, staph, and strep.

Similarly, many bacteria that cause disease primarily in the digestive tract—cholera, dysentery, E. coli, Enterobacteriaceae, Enterococcus faecium, klebsiella, proteus, pseudomonas, salmonella, Serratia marcenscens, and shigella—have mutated to become resistant to specific antibiotics. (For a lengthy but fascinating look at the world through the eyes of virologists, read Laurie Garrett’s The Coming Plague.)

In 1992, 13,300 hospital patients died of infections that resisted every drug doctors tried. Currently, forty thousand North Americans die each year from antibioticresistant infections. The sexual revolution also helped the evolution of microbes. Multiple sex partners allowed bacteria, fungi, and virus more opportunity to replicate, increasing the possibility of mutation.

Some of these mutant microbes became better at causing infection or deepening illness. Given people’s rapid movement between countries, these new microbes are spread quickly throughout the world, increasing the risk of even more mutation and enhancement of the microbial defense system.

In The Coming Plague, Laurie Garrett spends nearly seven hundred pages discussing microbes, their increasing virulence, and the devastation of their epidemics. Her solutions offer little optimism. But she has neglected half the equation. If microbes are becoming more resistant and virulent, we must increase our own resistance and strength to outsmart them.

We must boost immune function so that people will be less receptive to infection. We need to take a new look at Metchnikoff ’s work and at probiotic bacteria and the many immune-strengthening benefits they confer. Optimum nutrition is a logical starting point.

By definition, nutrients are essential for growth, immune function, repair, and maintenance of our bodies. But the diet of Americans will not protect our immune function. New research has shown that diets deficient in just one nutrient, in this case either selenium or vitamin E, could cause a benign virus to mutate to a diseaseproducing organism.

Today, 80 percent of women and children do not meet the recommended daily intake (RDI) for vitamin E and zinc. Eighty percent of American women do not meet the RDI for magnesium. A study of high school runners found that 45 percent of girls and 17 percent of boys were deficient in iron, while 31 percent of female college athletes were also found to be iron deficient.

A recent survey of nutritional status in elderly Americans showed that 25 percent were malnourished, and 50 percent of all hospitalized elderly suffer from malnutrition. Dysbiosis weakens our ability to protect ourselves from diseasecausing microbes, which are generally composed of low-virulence organisms.

Unlike salmonella, which causes immediate foodpoisoning reactions, low-virulence microbes are insidious. They cause chronic problems that go undiagnosed in the great majority of cases. If left unrecognized and untreated, they become deepseated and may cause chronic health problems, including joint pain, diarrhea, chronic fatigue syndrome, or colon disease.

Because most doctors in our culture do not yet recognize dysbiosis, symptoms are treated with medication, but the underlying cause is never dealt with, and ultimately people do not get well.

Published research has listed dysbiosis as the cause of arthritis, diarrhea, autoimmune illness, B12 deficiency, chronic fatigue syndrome, cystic acne, the early stages of colon and breast cancer, eczema, food allergy or sensitivity, inflammatory bowel disease, irritable bowel syndrome, psoriasis, and steatorrhea.

These problems were previously unrecognized as being microbial in origin. Common dysbiotic bacteria are aeromonas, citrobacter, helicobacter, klebsiella, salmonella, shigella, Staphylococcus aureus, vibrio, and yersinia.

Helicobacter, for example, is commonly found in people with ulcers. Citrobacter is implicated in diarrheal diseases. A common dysbiosis culprit, the candida fungus, causes a wide variety of symptoms that range from gas and bloating to depression, mood swings, and premenstrual syndrome (PMS).