Study links higher sugar intake during antibiotics to greater gut bacteria loss

Eating more sugar while taking antibiotics may intensify the disruption those drugs cause to beneficial gut bacteria, according to research published online Sept. 30, 2026, in the journal Nature. Researchers from NYU Langone Health, City of Hope and Memorial Sloan Kettering monitored 9,419 meals consumed by 173 hospitalized cancer patients and tracked changes in their gut microbiomes, the communities of bacteria that help with digestion and immune function.

For every additional 100 grams of sugar eaten during the 48 hours before treatment, the researchers observed an additional 21% decline in alpha diversity, a measure of the variety of beneficial bacterial species found in the gut. The findings also showed that sugary diets combined with antibiotic treatment were associated with increases in Enterococcus faecium among patients. This bacterial species has been linked to infections that can be difficult to treat.

Mouse experiments produced a similar result, according to the study. Animals exposed to the antibiotic biapenem while consuming dietary sucrose, a form of sugar, experienced a 16.3-fold increase in the gut Enterococcus population by day 3, and by day 6 the bacterial burden was 33.4-fold higher.

"As we are learning how collateral damage of antibiotics to the microbiome are linked with long-term health problems, it's important to identify factors that limit these unintended health risks," said the study's co-senior author Jonas Schluter, PhD, assistant professor in the Department of Microbiology at NYU Langone. He said the study suggests that modifying diet during and after antibiotics, specifically by reducing sweets intake, could help.

"The microbiome is emerging as an important factor in cancer care," said co-senior study author Marcel van den Brink, MD, PhD, chief physician executive at City of Hope. He said that for patients undergoing intensive treatments such as bone marrow transplantation, the healthy diversity of the gut microbiome can have important implications for outcomes.

The team focused on people with blood cancers because these patients frequently receive antibiotics and their food intake can be monitored closely during hospitalization, according to the study. Researchers recorded what patients ate at every meal and collected microbiome samples each day, a combination the study described as making the project one of the largest and most detailed of its kind to date. Patients with blood cancers who receive stem cell transplants are often hospitalized for several weeks while undergoing chemotherapy and antibiotic treatment, and their diets and gut microbiomes can change dramatically during that period.