Sweets during antibiotics linked to deeper microbiome injury

Clinical takeaway: Limiting sugary foods during antibiotic treatment may help to protect gut microbiome diversity. 

Every clinician who prescribes a broad-spectrum antibiotic accepts a tradeoff: the drug likely clears the infection but also strips away beneficial gut bacteria. Patients who lose the most microbial diversity tend to fare worse. Nothing in the standard playbook quantifies or addresses that collateral microbial damage. 

Diet shapes the gut microbiome, but most of that evidence comes from healthy volunteers with stable gut communities or from small dietary trials in chronic disease. What happens when food choices meet a microbiome already under assault hasn't been closely studied. New research takes up that question in hospitalized cancer patients, pairing meal-level dietary records with serial stool sampling, and it singles out one dietary component tied to deeper disruption when antibiotics are on board. 

For every 100 g of sugar-rich foods (roughly a large milkshake or 2–3 sodas) a patient consumed in the two days after broad-spectrum antibiotic exposure, the model predicted an additional 24.1% drop in mean gut bacterial diversity compared with unexposed samples. Sweets eaten without antibiotics on board showed no association with diversity at all, so the damage tracked the combination, not the sugar itself. The same interaction held when meals were recoded by macronutrient rather than food group, with sugars during antibiotic exposure predicting a further 20.6% diversity decrease per 100 g. 

The organism filling the vacuum was Enterococcus faecium, a leading cause of antibiotic-resistant bloodstream infections and a marker of graft-versus-host disease and mortality after transplant. Each additional 100 g of sweets during antibiotic exposure was associated with greater expansion of the species, and formulated nutritional beverages such as sports drinks and nutritional shakes ranked among the key contributors. In mice, sucrose supplementation amplified antibiotic-induced enterococcal expansion 16.3-fold at day three and 33.4-fold at day six, with no effect in the absence of antibiotics. 

"No matter how we analyzed the data, the same strong signal kept appearing," said co-senior author Marcel van den Brink, MD, PhD, president of City of Hope Los Angeles and the center's chief physician executive. "The patients who consumed more sweets while taking antibiotics were more likely to experience a loss of microbiome diversity as aggressive microbes crowded out other strains of bacteria." 

The researchers tracked 9,419 meals eaten by 173 patients hospitalized for allogeneic stem cell transplant, all of whom received at least one antibiotic and 80% of whom escalated to broad-spectrum agents. Meal trays arrived with item-level questionnaires completed at the bedside, yielding dietary records in dehydrated-weight grams. Bayesian models paired 1,009 stool samples from 158 patients with each sample's preceding two-day dietary window. 

The next test is already defined: prospective trials in transplant patients of whether cutting sugar during antibiotic courses preserves diversity and improves outcomes, a step the authors call readily evaluable across cohorts on various antibiotics. A nearer-term change may come to the hospital meal tray itself, since the nutritional shakes, smoothies, and sports drinks hospitals routinely hand inpatients sit squarely in the implicated category and could be eliminated when prescribing antibiotics. 

"It's premature to recommend everyone taking antibiotics avoid sugar," van den Brink said. "On the other hand, we don't have strong evidence that probiotics help preserve or restore microbiome diversity and many people choose to take them anyway. There's no harm in limiting sugar in your diet, and it's an easy thing to try." 

Source: Dai A, et al. (2026 Sep 30) Nature. Sugar-rich foods exacerbate antibiotic-induced microbiome disruption