A Nature study tracked more than 9,400 hospital meals eaten by transplant patients and found that sugar-rich foods on antibiotics went with sharper losses of gut bacterial diversity.
Antibiotics are among the most important drugs in medicine, but they come with collateral damage. Alongside the bacteria causing an infection, they kill many of the trillions of beneficial microbes that live in the gut. For most healthy people, that community recovers. For patients with weakened immune systems, the damage can be dangerous.
A new study suggests that what patients eat while taking antibiotics may influence how much harm is done. Researchers at City of Hope, Memorial Sloan Kettering Cancer Center and NYU Grossman School of Medicine report in Nature that patients who ate more sweets during antibiotic treatment lost more of their gut bacterial diversity.
“Antibiotics disrupt the diversity of our gut bacteria, or microbiomes, which play an essential role in supporting our immune systems and overall health,” said Marcel van den Brink, M.D., Ph.D., president of City of Hope Los Angeles and City of Hope chief physician executive, who co-led the work. “Our research supports emerging evidence that avoiding sugary foods during antibiotic treatment may protect the microbiome.”
A vulnerable group of patients
The study focused on people with blood cancers undergoing allogeneic hematopoietic cell transplant, in which a patient receives blood-forming stem cells from a donor. Before the transplant, patients receive intensive chemotherapy, sometimes with radiation, to wipe out their diseased bone marrow. They then spend weeks in hospital while the new cells take hold, with little immune protection.
Infections are a constant threat during that period, so antibiotics are routine. In this study, every patient received at least one antibiotic, and 80 percent received one or more broad-spectrum antibiotics, which kill a wide range of bacteria.
Transplant patients have become one of the clearest windows into how the gut microbiome affects health. Earlier research, including large studies involving the same research groups, has linked lower microbiome diversity during transplant to higher rates of complications and death. “Preserving microbiome diversity has previously been linked with improved clinical outcomes for patients with cancer,” van den Brink said.
One danger is domination by a single type of bacterium. When antibiotics clear out competitors, hardy microbes such as Enterococcus can take over the gut. In transplant patients, Enterococcus dominance is associated with higher risks of bloodstream infection, graft-versus-host disease and other serious complications. Some strains are resistant to vancomycin, an antibiotic often used as a last line of defence.
Counting every meal
Nutrition research often depends on what people remember eating, which is notoriously unreliable. The hospital setting allowed something far more precise. Over five years, the team tracked 9,419 meals eaten by 173 patients. Meal trays came with questionnaires about what was eaten and drunk, the hospital kitchen supplied nutritional information, and researchers recorded more than 40,000 individual food items.
Each patient had between 8 and 128 tracked meals, covering a period from 12 days before to 49 days after transplant. The researchers also profiled gut microbiome diversity in 158 of the patients using more than 1,000 stool samples.
“Unlike past nutrition studies that rely on patients’ memories of what they ate or other imprecise surveys, we had meticulous dietary records collected in real time,” van den Brink said. “This enabled us to look for patterns that otherwise might be impossible to detect.”
A consistent signal
The team analyzed the data with several statistical approaches. “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.”
The release puts a number on it: every additional 100 grams of sweets, roughly the amount in a large milkshake, was associated with a 24 percent drop in bacterial diversity during antibiotic treatment. The loss was linked to overgrowth of Enterococcus.
To test whether sugar could actually cause the effect, the researchers turned to mice. Healthy mice given broad-spectrum antibiotics and a high-sucrose diet developed Enterococcus overgrowth. Mice fed the same diet without antibiotics kept normal microbial diversity, suggesting that it is the combination of antibiotics and sugar that matters.
“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.
Rethinking the hospital tray
The findings raise practical questions for hospitals. “Many of the foods and drinks we encourage hospitalized patients to consume, like nutritional shakes, smoothies and sports drinks, are high in sugar content,” van den Brink said. “That’s something we’ll need to evaluate when prescribing antibiotics.”
The choice of antibiotic matters, too. “Antibiotic stewardship includes thinking about how different antibiotics affect the microbiome,” he said. “Our study demonstrates that some antibiotics disrupt beneficial gut bacteria more than others.” The release encourages patients to ask their care teams whether an antibiotic was chosen from among equally effective options.
Not yet a rule
Van den Brink is careful not to overstate the case. “It’s premature to recommend everyone taking antibiotics avoid sugar,” he said. The human data show an association rather than proof of cause, and the patients in the study were a highly specific group, seriously ill and heavily treated in hospital. Whether the same pattern holds for a healthy person taking a short course of antibiotics for a sinus infection is unknown.
Still, van den Brink notes that the downside of cutting back is small. “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,” he said. “There’s no harm in limiting sugar in your diet, and it’s an easy thing to try.”
The study was co-led by Jonathan Peled, M.D., Ph.D., of Memorial Sloan Kettering and Jonas Schluter, Ph.D., of NYU Grossman School of Medicine, and supported by the National Cancer Institute, the National Heart, Lung and Blood Institute and Memorial Sloan Kettering’s Susan and Peter Solomon Microbiome, Nutrition and Cancer Program.
“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.”
Notes
- “Sugar-rich foods exacerbate antibiotic-induced microbiome injury.” Nature, 30 September 2026. DOI: 10.1038/s41586-026-11077-3.
- City of Hope. “Study suggests skipping sweets during antibiotic treatment may help protect the gut microbiome.” EurekAlert!, 30 September 2026. https://www.eurekalert.org/news-releases/1145587.
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