In 2015, Sandy Lewis, a small-time organic cattle farmer in upstate New York, bought 13 bulls, for around $5,000 each, from a breeder in Oklahoma. A few weeks after the animals were trucked to his farm near the Vermont border, Mr. Lewis discovered that two of the bulls had died. He could see holes in their abdomens from where they had gored one other.

A field autopsy proved inconclusive. When two more bulls among the new herd fell sick, Mr. Lewis shipped them off to Cornell University to be examined. One died along the way, but a blood test on the living bull provided the answer: It had anaplasmosis, a bacterial illness that destroys red blood cells and deprives the animals of oxygen, causing them at times to act violently. The disease is relatively rare in the Northeast, yet a quarter of Mr. Lewis’s herd ended up becoming infected. He lost another six animals to the disease and spent more than $100,000 trying to save the rest. Ultimately, another 100 animals had to be culled.

The costly experience propelled Mr. Lewis, an intense, cranky and compulsive former Wall Street arbitrageur, on a two-year investigative journey into the use of antibiotics on American animal farms. Now he is asking a question he believes government regulators and the meat industry urgently need to grapple with: Are pig, cattle and poultry farmers misusing antibiotics, allowing too much of the drug to get into our food?

It has long been common knowledge in farming that antibiotics can help cause animals to grow fatter faster. Time is money, particularly in the food industry, and for many years ranchers used antibiotics not just for treating diseases but also for promoting growth so that animals would be ready for the slaughterhouse sooner. (Mr. Lewis says his grass-fed steers require 27 months to get to market without antibiotics, more than twice as long as it takes cows pumped full of antibiotics.)

In early 2017, the Food and Drug Administration enacted rules banning the use of human antibiotics purely for growth promotion in animals and requiring ranchers to get a prescription from a veterinarian for antibiotics that once could be purchased over the counter. The F.D.A. enacted the restrictions out of growing concern about the breeding of drug-resistant bacteria from antibiotic overuse. Those resistant bacterial strains can be transferred to humans by contact with animals or raw meat and possibly through the consumption of undercooked meat.

The growing resistance of bacteria to antibiotics causes some 23,000 American deaths a year and $34 billion in financial losses annually, according to the Centers for Disease Control and Prevention. The C.D.C. also estimates that more than 400,000 United States residents become ill with infections caused by antibiotic-resistant food-borne bacteria every year, with about one in five resistant infections caused by germs from food and animals.

“Antibiotic resistance is of great public health concern because the antibiotic-resistant bacteria associated with the animals may be pathogenic to humans, easily transmitted to humans via food chains, and widely disseminated in the environment via animal wastes,” South African researchers observed in a recent article published in the journal Molecules.

Despite the ban, Mr. Lewis is convinced that some ranchers continue to use antibiotics for growth purposes — a claim that is difficult to document. But experts agree that the F.D.A. rules have a “giant loophole” that allows farmers to continue to use antibiotics to prevent diseases even if animals aren’t showing symptoms.

“You don’t even need a sick animal in the herd to use antibiotics in the feed and water as long as the justification is ‘disease prevention’ not ‘growth promotion,’ ” Avinash Kar, a senior attorney at the Natural Resources Defense Council, told me.

Veterinarians working for certain feedlots — industrial-style farms where chickens, pigs and cattle are fattened — seem more than happy to continue writing prescriptions for antibiotics that end up in livestock feed. “They’ve got their veterinarians on retainer,” Mike Callicrate, a cattle rancher in Kansas and Colorado, told me. “They tell them what they want, and the veterinarian darn well provides what they want.”

Veterinarians deny this. Dr. Lloyd Barker, the veterinarian to the rancher who sold animals to Mr. Lewis, said vets are “toeing the line” and added, “Our primary goal is prevention.”

Mr. Kar said that of all the “medically important” antibiotics sold in the United States — that is, those used to treat human disease — about 70 percent goes into the feed and water of animals, indicating to him that overuse on the farm is still rampant.

It is difficult to document antibiotics abuse, however, because the F.D.A. does not collect data on the reason for the use of the drugs. But the agency says that it is working to obtain better data to help monitor potential misuse.

Beyond the threat of drug-resistant illness, there is evidence of another risk from antibiotic overuse in pigs, poultry and cattle: the possibility that people who consume antibiotic-laced meat will get some of the drugs, as well as resistant bacteria, into their own digestive tracts — with potentially harmful results.

A growing body of scientific research also shows that the antibiotics we take as medicine can disrupt our so-called gut microbiome, the bacteria that live happily in our stomach and intestines and that are the key to our ability to properly digest food and process fats. This disruption has been linked to the rise of noncommunicable diseases such as obesity, juvenile diabetes, asthma and allergies. Some researchers also believe that alterations in the gut microbiome have led to an increase in the incidence of autism, Alzheimer’s and Parkinson’s disease.

“Antimicrobials or antibiotics given early in life can have significant implications upon obesity, on diabetes, upon the propensity for other diseases,” explained Jack Gilbert, the faculty director of the Microbiome Center at the University of Chicago.

Mr. Lewis, 79, and the son of the onetime managing partner of the now-defunct Bear Stearns investment bank, grew up on Park Avenue, though he says he never quite fit in. Still, after studying at the Orthogenic School with Bruno Bettelheim, who taught him to “never care what others think,” Mr. Lewis made a fortune on Wall Street. He ran afoul of the law there, pleading guilty to stock manipulation in 1989 and receiving three years probation. (He argues — and a federal judge agreed — that he never made a dime on the manipulation and was only trying to punish traders who reaped profits at the public’s expense.) In 2001, President Bill Clinton gave him a full pardon, and in 2006 the Securities and Exchange Commission vacated his lifetime ban from the securities industry.

In 2004, Mr. Lewis decamped with his wife, Barbara, to Essex, N.Y., to try his hand at farming, acquiring a 1,100-acre farm just west of Lake Champlain. He has 520 head of grass-fed cattle that he raises and sells for beef to customers like Middlebury College and Deerfield Academy. (I met him a decade ago while researching a book on Bear Stearns.)

Much of his time these days is spent trying to persuade ranchers, veterinarians, agriculture experts and environmental groups — really, anyone who will listen — of the dangers of antibiotic misuse. He has called on the F.D.A. to close the loophole that allows ranchers to feed antibiotics to their animals prophylactically, and for violations to be a criminal offense.

Mr. Lewis also said there is another way to prevent antibiotic drugs from possibly harming the human gut microbiome: injecting them rather than ingesting them in pill form. Some researchers believe that injections get the drug into the body with little or no damage to the gut microbiome, while ingested antibiotic pills go straight into the digestive tract. Shots can also deliver lower doses of antibiotics and work faster than pills.

The effectiveness of the approach is widely disputed. Getting big animals like cows and pigs to cooperate long enough for a shot is expensive, time consuming and plain hard work. (Few farmers have Mr. Lewis’s resources.) It’s also much easier for a doctor to prescribe a course of antibiotic pills to people battling infection than to arrange for a series of shots.

Dr. Hua Helen Wang, a professor in the microbiology department at Ohio State University who has done pioneering research into the benefits of taking antibiotics by injection, told me that while more studies need to be done, there is no question that taking antibiotics in pill form should be limited to treating infections in the gastrointestinal tract. In a 2013 paperpublished by the American Society for Microbiology, Dr. Wang and her team determined that injected antibiotics reduced the spread of antibiotic-resistant genes in the guts of mice better than orally administered drugs. The injections also protected the integrity of the gut microbiota, they found. “This is a landmark breakthrough,” Dr. Wang said.

But Dr. Martin J. Blaser, a professor of microbiology at New York University, the author of “Missing Microbes” and the nation’s leading authority on the risks of antibiotic use on the microbiome, says that even if antibiotics are administered by injection, some of the drug still finds its way into the digestive tract.

Dr. Blaser’s bigger concern is doctors’ reluctance to change ingrained behavior regarding the prescription of antibiotics to both humans and animals. “People worry that if we use less antibiotics there will be more bad infections, uncontrolled infections,” he said. He points to Sweden, where on a per capita basis people use about 40 percent of the antibiotics we use in this country. “There are no epidemics of infections in Sweden,” he said.

Mr. Kar, at the N.R.D.C., notes that Denmark uses about 30 percent lessantibiotics a year on a per-kilogram of meat basis than American farms do. But he applauds the fact that big chicken producers like Perdue, Tyson and Foster Farms have reduced or eliminated antibiotic use in the feed, perhaps under pressure from their biggest customers, including KFC, McDonald’s and Subway, which now claim in their advertising that all or some of the chicken they serve has been raised without antibiotics. He thinks beef and pork producers should follow suit.

Mr. Lewis, meanwhile, argues that the continued destruction of the smallest bacteria in our gut biomes risks deadly epidemics of chronic or drug-resistant diseases. That may be hyperbole, but there is wide agreement that antibiotic overuse in both livestock and in people is destroying our ability to fight certain diseases and infections.

And he’s got a message for his fellow cattle ranchers. Their misuse of antibiotics, he says, makes “arbitrage look honest.”