Stanley Falkow was a professor emeritus of microbiology and immunology at the Stanford University School of Medicine. (Linda A. Cicero/Stanford News Service)

Stanley Falkow, a microbiologist who uncovered the molecular underpinnings of infectious diseases, sounded the alarm for antibiotic-resistant bacteria and championed the benefits of microorganisms in the gut and even in stool, died May 5 at his home in Portola Valley, Calif. He was 84.

The cause was complications of myelodysplastic syndrome, a bone marrow disorder, said his wife, Lucy Tompkins.

Dr. Falkow (pronounced falk-oh) was a professor emeritus of microbiology and immunology at the Stanford University School of Medicine. He had studied microbes since he was 11, when he trained a microscope on a cup of spoiled milk, and overcame debilitating social anxiety to become one of the most acclaimed researchers in his field and a mentor to more than 100 students.

In 2008, he was honored with the Lasker-Koshland Special Achievement Award in Medical Science, part of a group of honors described as America’s Nobel Prizes. The award citation called him “one of the great microbe hunters of all time,” and the “founder of molecular microbial pathogenesis,” the study of how pathogens cause disease.

Though he focused on their relation to human illness, Dr. Falkow maintained a seven-decade love affair with microbes of all kinds, and proclaimed the wonders of everything “from the mites that inhabit the eyebrows to the seething cauldron of more than 600 species of bacteria that inhabit the large bowel.”

His most influential work centered on plasmids, circular DNA molecules inside bacterial cells. He showed they could transfer significant traits from one bacteria to another — including resistance to antibiotics or the ability to create disease-inducing toxins. Such gene transfers can enable a once-benign bacteria to become a threat to human health.

While Dr. Falkow began his research with a focus on gonorrhea, he went on to identify a strain of E. coli bacteria responsible for debilitating diarrhea, and helped unravel the molecular origins of ailments including plague, whooping cough, cholera, tuberculosis, typhoid fever, ulcers, food poisoning and urinary tract infections.

“He was basically trying to write the operating manual for disease-causing bacteria,” said David A. Relman, a former student of Dr. Falkow’s and a Stanford professor of microbiology and immunology. “You can think of it as the operating manual for a car. With that, you understand how it works and how to fix it. In this case you know how microbes operate, and then how to attack them or block them.”

Dr. Falkow devised a set of criteria, known as molecular Koch’s postulates, to determine which of a pathogen’s genes contribute to a disease. His research also laid the foundation for the earliest experiments on recombinant DNA, which combines genes from different organisms. Doing so enables scientists to isolate genes and determine their function.

Beyond his laboratory research, Dr. Falkow served on scientific committees and testified before Congress on the dangers of routine antibiotic use in animal feed, which can engender resistance to the drugs. “He was pissed off to the end,” his wife said, that antibiotics were still used in medically unnecessary situations.

Fighting infectious diseases, Dr. Falkow said in his Lasker acceptance speech, was not merely “a matter of them versus us, or a war of attrition. Rather, based on cell number, each of us is more microbial than human; we carry ten times more microbial cells than cells of our own. The human body is a biological universe of many species, most of which have never been grown in the laboratory and whose role in health and disease is still a mystery.”

Stanley Falkow was born in Albany, N.Y., on Jan. 24, 1934. He grew up in a Yiddish-speaking household where his father was a shoe salesman who emigrated from Kiev, Ukraine. His mother, the daughter of Jewish immigrants from Poland, rented several of their bedrooms and later opened a corset shop.

Dr. Falkow became interested in science soon after the family moved to Newport, R.I., in 1943, where he discovered Paul de Kruif’s book “Microbe Hunters” at the public library. He had poor grades until his senior year of high school, however, leading an adviser to suggest he consider the military rather than college.

He instead enrolled at the University of Maine, which had a bacteriology department. During his summers he worked at the hospital in Newport, developing slides and assisting in the occasional autopsy.

After graduating in 1955, he studied at the University of Michigan before dropping out because of recurring panic attacks. He eventually received his doctorate in biology at Brown University in 1961, and worked at the Walter Reed Army Institute of Research.

For years, he wrote, he lived “both scientifically and personally in a kind of cocoon, always half afraid and ready at a moment’s notice to run” because of his anxiety attacks. He said he was more comfortable at his microscope than around people, and tried to imagine that he himself was a microbe in an effort to understand how they dealt with their human hosts.

Dr. Falkow said his anxiety diminished somewhat after a colleague taught him to fly fish, and after he forced himself to attend and speak at academic conferences.

His marriage to Rhoda Ostroff ended in divorce, and in 1983 he married Tompkins, a former graduate student who is now an infectious diseases specialist at Stanford. In addition to his wife, of Portola Valley, survivors include two daughters from his earlier marriage; a stepson; a sister; and four grandchildren.

Dr. Falkow was on the faculty of Georgetown University and the University of Washington before joining Stanford in 1981 as chair of microbiology and immunology. He retired after being diagnosed with myelodysplastic syndrome in 2004, when doctors told him he had two years to live.

He received the Robert Koch Award for medical research in 2000 and the National Medal of Science in 2016.

His wife said that in the last several years, Dr. Falkow was contacted each October by the Stanford communications office, asking how it might reach him if he was awarded the Nobel Prize — an honor that many colleagues believed he was due to receive.

It was not one he wanted. “He’d tell me, ‘I absolutely don’t want it. It’s not who I am; it would change who I am. I’d be trotted out all over the place. I do not want it,’ ” Tompkins said.

Four days before Dr. Falkow died, he told his wife: “At least now I won’t get the Nobel Prize.”