Sugar Intake Before Antibiotics Linked to Gut Microbiome Damage

Researchers from Memorial Sloan Kettering Cancer Center, NYU Langone Health and City of Hope reported in the journal Nature on September 30, 2026, that eating sugar-rich foods during antibiotic treatment worsens the disruption antibiotics cause to the gut microbiome, based on a five-year study of 173 hospitalized patients undergoing stem-cell transplantation for blood cancers.¹³⁴⁵

The study

The research team tracked 9,419 recorded meals among the 173 allogeneic haematopoietic cell transplantation (allo-HCT) recipients and analysed microbiome data from 158 of them, drawing on 1,009 stool samples. Researchers characterized the project as one of the biggest and most detailed studies of its type conducted so far, noting that its careful, real-time tracking of meals gave nutrition research a level of precision rarely achieved before.⁵⁶

About 80 percent of patients were switched from prophylactic to broad-spectrum antibiotics during their hospital stay. The researchers found that shifts in microbiome composition were moderately associated with shifts in dietary composition from baseline.¹⁵⁶

Sugar and diversity loss

According to the Nature study, each 100 grams of sugar eaten while patients were on antibiotics corresponded to a further 24.1 percent drop in bacterial alpha-diversity, while a companion report from NYU Langone Health and GRAIL cited a 21 percent figure tied to sugar eaten within two days prior to starting treatment. Sugar intake during antibiotic exposure was found to be significantly additive to the diversity reduction already caused by the drugs.¹³⁴

Eating high-sugar foods alongside broad-spectrum antibiotics was also linked to surges of Enterococcus faecium, a bacterium capable of causing infections acquired in hospitals. In mouse experiments, combining the antibiotic biapenem with a high-sucrose diet produced a 16.3-fold increase in Enterococcus by day three, rising further by day six, while mice fed a high-sugar diet without antibiotics maintained normal bacterial diversity.¹³⁴⁵

Among patients with above-median sugar intake, each additional day of antibiotic exposure was associated with a higher mortality risk; no such association appeared in the below-median sugar intake group. Microbiome injury in blood cancer patients has separately been associated with higher overall mortality and infections.¹³⁴

Clinical implications

Sugar-enriched oral nutritional supplements, such as shakes, smoothies and sports drinks, are commonly recommended to transplant recipients to help maintain nutritional intake, the researchers noted, even though these products are typically high in sugar.¹⁵

Jonathan Peled remarked that "Many of us are motivated to find ways to protect the microbiome when we or our children are prescribed antibiotics," and further noted that "Limiting the intake of sugary foods offers a potential way to do that. Peled added, "It's very feasible, likely to be very low toxicity, very tolerable and very economical."²

Marcel van den Brink said the same signal appeared across multiple analyses of the data, stating, "No matter how we analyzed the data, the same strong signal kept appearing," and that "The patients who consumed more sweets while taking antibiotics were more likely to experience a loss of microbiome diversity." He cautioned, however, "It's premature to recommend everyone taking antibiotics avoid sugar. He added, "There's no harm in limiting sugar in your diet."⁵

William Jogia, the paper's second author, acknowledged uncertainty about how sugar affects the microbiome, stating: "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." Peled indicated that a key next step would involve designing clinical trials to determine whether reducing sugar intake for a short period can lead to better patient outcomes.³