Consuming sugary foods while taking antibiotics significantly worsens gut microbiome disruption, according to a study published on September 30, 2026, in Nature. Researchers at City of Hope, Memorial Sloan Kettering Cancer Center, and NYU Langone Health found that high-sugar diets paired with broad-spectrum antibiotics accelerated the loss of bacterial diversity and fueled the overgrowth of dangerous pathogens.
Tracking Meal Data Across Hospital Stays
According to Jonathan Peled, MD, PhD, and lead author Anqi Dai, MA, researchers tracked 173 hospitalized patients with blood cancers undergoing allogeneic hematopoietic cell transplants—an intensive medical procedure that wipes out the immune system with heavy chemotherapy, sometimes accompanied by radiation, and requires heavy antibiotic use. The findings stem from an inpatient study conducted between 2017 and 2022 at Memorial Sloan Kettering Cancer Center in New York, where adult allogeneic hematopoietic cell transplant recipients were admitted for intensive treatment. Because patients remained hospitalized for weeks, the research team captured an unprecedented dataset of dietary habits and microbial shifts.
Patients marked meal trays immediately after eating to indicate via hospital kitchen Computrition software printouts whether they consumed 0, 25, 50, 75, or 100 percent of each item ordered. Hospital kitchen records and recipes provided precise nutritional values, allowing dietitians and scientists to analyze more than 40,000 food items assigned eight-digit food codes according to FNDDS46 classifications across 9,419 recorded meals spanning between 8 and 128 meals per patient from 12 days before to 49 days after transplantation. Researchers also collected and analyzed 1,009 stool samples from 158 of the patients to monitor daily fluctuations in gut bacteria.
How Sugar Multiplies Antibiotic Damage
While antibiotics are essential for treating infections by wiping out harmful bacteria, they inflict collateral damage on helpful microorganisms that support human immunity and health. The new data revealed that adding sweets and sugary drinks to the equation dramatically amplifies that destruction.
For every 100 grams of sugar consumed in the 48 hours before treatment, patients experienced an additional 21 percent reduction in alpha diversity—a standard measure of the variety of helpful bacterial species present in the digestive tract. Separate dietary categorization modeled by the team showed a similar drop of 24 percent in bacterial diversity for every 100-gram increase in foods classified under sweets and sugary drinks, measured after removing water content and equivalent in sugar content roughly to a large milkshake.
“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.”
Jonas Schluter, PhD, NYU Langone Health
Growth of Enterococcus Faecium
One specific bacterial species stood out across the analysis: Enterococcus faecium. The combination of high-sugar diets and broad-spectrum antibiotics—administered to 80 percent of the study participants who were switched after a fever or other sign of infection—created fertile ground for aggressive microbes to crowd out beneficial strains.
When Enterococcus takes over the digestive tract, transplant patients face bloodstream infections and other complications. To test whether sugar directly drove this bacterial bloom, researchers conducted companion experiments in mice. Healthy mice given the antibiotic biapenem alongside a dietary sucrose high-sugar diet developed a massive overgrowth of Enterococcus in their guts—scaling up to 16.3-fold by day 3 and 33.4-fold higher burden by day 6 compared to mice receiving antibiotics alone. When mice consumed the high-sugar diet without antibiotics, their bacterial diversity remained normal.
“Our research supports emerging evidence that avoiding sugary foods during antibiotic treatment may protect the microbiome. Preserving microbiome diversity has previously been linked with improved clinical outcomes for patients with cancer.”
Marcel van den Brink, MD, PhD, City of Hope
Dietary Adjustments in Clinical Care
The study authors emphasize that while the retrospective data strongly links sugar intake to severe microbiome disruption during antibiotic courses, further clinical trials are necessary to prove whether short-term dietary modifications directly improve patient survival rates and recovery outcomes.
Researchers suggest that modifying diet during and after antibiotic treatments by cutting back on sweets could offer a way to help protect intestinal health. Among patients in the hospital cohort, prolonged exposure to broad-spectrum antibiotics combined with sugar-enriched diets predicted the risk of death.