Sweets while on antibiotics: in 9,419 hospital meals, sugar went with deeper damage to the gut's bacteria

Antibiotics clear harmful bacteria, but they also thin out the trillions of helpful ones in the gut. When that community loses variety, a few hardy species can take over. One of them, Enterococcus, is a common cause of hard-to-treat infections in hospital. Fibre is known to help the gut recover after antibiotics. Far less was known about whether anything else people eat during a course makes the damage better or worse.

A study published in Nature on 30 September 2026, led from NYU Langone Health with Memorial Sloan Kettering Cancer Center and City of Hope, looked at people having an allogeneic stem cell (bone marrow) transplant for blood cancer at Memorial Sloan Kettering between 2017 and 2022. These patients stay in hospital for weeks, often need antibiotics, and eat from a hospital menu, so the team could record food precisely: after every meal, patients marked how much of each item they had eaten, and a dietitian checked the records. In all, 9,419 meals from 173 patients were matched with more than 1,000 stool samples from 158 of them.

On their own, foods in the sugars, sweets and sweet drinks group were not linked to lower gut bacterial diversity. Eaten in the two days before a sample taken after broad-spectrum antibiotics, they were. Each extra 100 g of these foods (measured as dry weight) went with a further 24% drop in diversity on top of the antibiotics' own effect, and a model based on sugar itself gave a 21% drop per 100 g. The same combination went with gut communities dominated by Enterococcus faecium. Added sugars and formulated drinks, such as sports drinks and nutritional shakes, contributed more than sugars found naturally in food. The authors note this was unexpected because sugary nutrition drinks are often recommended to transplant patients.

To test cause and effect, the team gave mice an antibiotic with or without sucrose (table sugar) in their diet. Sugar alone made no difference, but with the antibiotic it boosted the Enterococcus bloom 16.3-fold at day 3 and 33.4-fold at day 6. Glucose and fructose, and blended fruit puree, did the same in mice, and the effect held on a fibre-free diet. The human part is observational and from a very sick group: almost all patients took a preventive antibiotic, strong antibiotics are started when someone is more unwell, and food brought from outside was not fully recorded. The authors say trials are needed before changing advice for transplant patients, though they suggest that limiting sugar during antibiotic treatment may help protect the gut's bacteria.