Sugar May Worsen Antibiotic Damage to Your Gut

Antibiotics already come with a well-known tradeoff: they kill harmful bacteria, but they take out beneficial ones too. New research suggests what you eat while taking them might make that tradeoff considerably worse.

Tracking Over 9,000 Meals

Researchers from NYU Langone Health, City of Hope, and Memorial Sloan Kettering Cancer Center closely monitored 9,419 individual meals eaten by 173 hospitalized cancer patients, tracking exactly what each patient ate alongside daily changes in their gut microbiomes. The team focused on blood cancer patients specifically because they frequently receive antibiotics during hospitalization and their food intake can be monitored with unusual precision throughout treatment. That combination of detailed diet records and daily biological sampling made the project one of the largest and most detailed studies of its kind to date.

A Clear Dose-Response Pattern

The results showed a clear relationship: for every additional 100 grams of sugar a patient ate in the 48 hours before antibiotic treatment, researchers observed an additional 21 percent decline in alpha diversity, a standard measure of how many different beneficial bacterial species are present in the gut. Sugary diets combined with antibiotic treatment were also linked to increases in a bacterial species called Enterococcus faecium, which has been associated with infections that can be genuinely difficult to treat. The findings were published online on September 30 in the journal Nature.

Confirming the Pattern in Mice

To test whether sugar was actually driving this effect, researchers ran a parallel experiment in mice. Animals given the antibiotic biapenem while also consuming dietary sucrose showed a 16.3-fold increase in their gut Enterococcus population by day three of the study. By day six, that bacterial burden had climbed to 33.4 times higher than baseline, a rapid and substantial expansion that closely paralleled what researchers observed in the human patients.

Why Sugar Might Make Things Worse

A healthy, diverse microbiome is generally better equipped to resist harmful bacteria gaining a foothold. Antibiotic treatment reduces that diversity, leaving the gut ecosystem more vulnerable overall. Researchers believe dietary sugar may amplify this vulnerability because the potentially harmful bacteria that survive antibiotic treatment can use those sugars as fuel to expand their numbers. William Jogia, a PhD student in the lab of study co-senior author Jonas Schluter and the paper’s second author, said it remains unclear whether sugar directly supports Enterococcus growth, weakens the bacteria competing against it, or works through some other mechanism entirely within actual patients.

A Simple Change With Real Implications

Jonas Schluter, assistant professor in the Department of Microbiology at NYU Langone and the study’s co-senior author, said that as researchers increasingly understand how collateral damage from antibiotics to the microbiome connects to long-term health problems, identifying factors that limit these unintended risks becomes genuinely important. He said the study’s scale, built on more than 9,000 recorded meals, suggests that modifying diet during and after antibiotic treatment, specifically by reducing sweets intake, could help address that risk. Marcel van den Brink, chief physician executive at City of Hope and another co-senior author, noted the microbiome is emerging as an important factor in cancer care more broadly, particularly for patients undergoing intensive treatments like bone marrow transplantation, where a healthy, diverse gut microbiome can meaningfully affect outcomes.

What Still Needs to Be Tested

Jonathan Peled, associate director of the Center for Hematological Malignancies at Memorial Sloan Kettering and a co-senior author, pointed out that microbiome injury in blood cancer patients specifically is already associated with worse outcomes, including higher overall mortality and more frequent infections. He said the logical next step is designing clinical trials to directly test whether short-term dietary changes can actually improve clinical outcomes for patients, rather than simply correlating with healthier microbiome measurements. For now, the researchers emphasize that more work is needed to pin down exactly how sugar produces this effect, and whether cutting back on sweets during antibiotic treatment will meaningfully improve how patients recover.

Sources

This report draws on the official announcement from NYU Langone Health and NYU Grossman School of Medicine, covering the peer-reviewed study by Dai, Ballweg, Jogia, and colleagues, published in Nature (2026).