American researchers have recommended temporarily cutting back on the sweet stuff during antibiotic treatment, saying that more sugar was linked to greater disruption of the gut microbiome and increased growth of potentially harmful bacteria, and that slashing sugar consumption was a simple way to reduce this damage.
Their study – published in the journal Nature – focused on the intestinal microbiome, the vast community of bacteria that has evolved alongside humans and helps with digestion, immune function and other essential processes.
Antibiotics are among the most commonly prescribed medicines worldwide, but they can kill beneficial bacteria as well as harmful ones. In some cases, that disruption also allows potentially dangerous species to gain an advantage.
A diverse microbiome is generally better able to resist the expansion of harmful pathogens. Antibiotic treatment can reduce that diversity, leaving the gut ecosystem more vulnerable to disease, according to the researchers.
Linked to greater microbiome damage
The researchers, from NYU Langone Health, City of Hope and Memorial Sloan Kettering, closely monitored 9 419 meals consumed by 173 hospitalised cancer patients and tracked changes in their gut microbiomes.
For every additional 100 grams of sugar eaten during the 48 hours before treatment, they 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. Animals exposed to the antibiotic biapenem while consuming dietary sucrose experienced a 16.3-fold increase in the gut Enterococcus population by day three of the study. By day six, the bacterial burden was 33.4-fold higher.
“As we are learning how collateral damage of antibiotics to the microbiome is linked to 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.
“Our study, which used more than 9 000 recorded meals, suggests that modifying diet during and after antibiotics, specifically by reducing sweets intake, could help with that.”
Why blood cancer patients
The team focused on people with blood cancers because these patients frequently receive antibiotics and their food intake can be monitored closely during hospitalisation. Researchers recorded what patients ate at every meal and collected microbiome samples daily.
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.
“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. “For patients undergoing intensive treatments like bone marrow transplantation, the healthy diversity of the gut microbiome can have important implications for outcomes. Studies like this help us better understand how everyday factors, including diet, may affect a delicate balance that influences how patients respond to treatment, recover, and experience side effects.”
Patients with blood cancers who receive stem cell transplants are often hospitalised for several weeks while undergoing chemotherapy and antibiotic treatment. During that period, both their diets and their gut microbiomes can change dramatically.
Potentially harmful species like Enterococcus faecium can flourish after much of the surrounding microbial ecosystem has been “destroyed”
Gut microbiome damage and cancer outcomes
The team said an important next step would be to design clinical trials to test whether short-term dietary changes can improve clinical outcomes.
Dietary sugar may magnify the microbiome disruption caused by antibiotics because potentially harmful bacteria that survive treatment may be able to use those sugars to expand, they noted.
“The new work identifies dietary sugars as an amplifier of antibiotic-induced microbiome disruption, probably because the potentially harmful bacteria that survive the antibiotics are benefiting from the dietary sugars they can use to expand,” said study second author William Jogia, a PhD student in Schluter’s lab in the Institute for Systems Genetics.
“While the findings suggest that reducing simple sugars may limit microbiome injury, whether sugar directly supports Enterococcus, weakens competing bacteria, or acts through another mechanism in patients remains to be seen.”
The researchers said more work was needed to determine exactly how sugar produces the effect and whether dietary changes will improve outcomes in patients.
Study details
Sugar-rich foods exacerbate antibiotic-induced microbiome disruption
Anqi Dai, Annamaria Ballweg, William Jogia et al.
Published in Nature on 30 September 2026
Abstract
Diet shapes the composition of the gut microbiota; however, the specific effects of distinct food groups on microbiome dynamics are unclear, particularly in circumstances of extreme perturbation. Here we evaluated the relationship between diet and intestinal microbiome dynamics by precisely tracking 9,419 meals consumed by 173 patients who were hospitalised for haematopoietic cell transplantation and analysing subsequent microbiome changes. Bayesian inference applied to data from 158 patients with paired longitudinal microbiome samples revealed that the intake of sweets and sugars during antibiotic exposure predicted exacerbated microbial dysbiosis, manifesting as lowered α-diversity and greater expansion of the pathobiont Enterococcus. Experiments in mice also showed that sucrose supplementation increased and prolonged antibiotic-induced Enterococcus expansion. These data suggest that avoiding a diet rich in simple sugars during antibiotic treatment may mitigate microbiota disruption. Further studies in independent cohorts will offer opportunities to generalise these findings and evaluate microbiota-sparing interventions.
Nature article – Sugar-rich foods exacerbate antibiotic-induced microbiome disruption (Open access)
See more from MedicalBrief archives:
Antibiotics may increase, not reduce, risk of further UTIs – Harvard/MIT/Washington study
Gut health, metabolism, disrupted by sweeteners – US review
Scientists warn cake and drinks sweetener can ‘damage gut wall’