Every patient took at least one antibiotic during their hospital stay to prevent or treat infections. About 80% received one or more broad-spectrum antibiotics, which target many types of bacteria at once and hit the microbiome hardest.

Sugar stood out — again and again

Using a range of statistical models, the researchers searched the dataset for patterns linked to microbiome injury. One signal kept surfacing.

"No matter how we analyzed the data, the same strong signal kept appearing," van den Brink said. "The patients who consumed more sweets while taking antibiotics were more likely to experience a loss of microbiome diversity as aggressive microbes crowded out other strains of bacteria."

One microbe stood out: Enterococcus. When this bacterium dominates the gut microbiome, transplant patients face a higher risk of bloodstream infections, graft-versus-host disease (a condition in which donor immune cells attack the patient's tissues), and other life-threatening complications.

The pattern was not subtle. Combining high-sugar foods with broad-spectrum antibiotics appeared to multiply the damage, producing that 24% loss of bacterial diversity per 100-gram increase in sweets.

Mice confirm the pattern

To test whether sugar actively worsens microbiome injury, the researchers gave broad-spectrum antibiotics to healthy mice and fed them various diets. Mice on a high-sucrose diet quickly developed Enterococcus overgrowth in their guts. Mice eating the same high-sugar diet without antibiotics maintained normal bacterial diversity — suggesting the combination, not sugar alone, drives the damage.

"The fact that animal studies support associations we found in patient data provides a compelling rationale for future clinical trials to evaluate whether reducing sugar intake during antibiotic use would protect the microbiome," van den Brink said.

He collaborated on the research with Jonathan Peled, M.D., Ph.D., of Memorial Sloan Kettering Cancer Center and Jonas Schluter, Ph.D., of NYU's Grossman School of Medicine.

What this means for patients and doctors

The findings connect to the growing idea of "food as medicine" during cancer care, and they could shape treatment strategies for cancer patients — and potentially for anyone taking antibiotics.

"The microbiome is emerging as an important factor in cancer care," van den Brink said. "The better we understand what supports and disrupts it, the more opportunities we have to reduce treatment side effects while improving how patients respond to and recover from therapy."

The results carry an immediate practical wrinkle for hospitals. Many foods and drinks commonly encouraged for hospitalized patients — nutritional shakes, smoothies, and sports drinks — are high in sugar. "That's something we'll need to evaluate when prescribing antibiotics," van den Brink noted.

For physicians, he said, the takeaway is that antibiotic stewardship should extend beyond preventing antibiotic resistance. "Antibiotic stewardship includes thinking about how different antibiotics affect the microbiome," he explained. "Our study demonstrates that some antibiotics disrupt beneficial gut bacteria more than others." He encourages patients to ask their care team to choose antibiotics thoughtfully from among equally effective options.

Should everyone on antibiotics cut sugar?

Not yet, according to the researchers. "It's premature to recommend everyone taking antibiotics avoid sugar," van den Brink cautioned. "On the other hand, we don't have strong evidence that probiotics help preserve or restore microbiome diversity and many people choose to take them anyway. There's no harm in limiting sugar in your diet, and it's an easy thing to try."

The study has clear limitations to keep in mind. The patient population was specific — people with blood cancer undergoing transplant — and the findings are associations supported by mouse experiments, not the results of a controlled trial testing sugar restriction. Whether cutting sugar protects the microbiome in the broader population of antibiotic users remains an open question, one the researchers say future clinical trials should address.