By Angela Dowden —
When you pick up an antibiotic prescription, dietary advice usually focuses on whether to take the pills on an empty stomach or with a meal. But could what you eat during treatment change how much those drugs disrupt your gut bacteria?
A study published in Nature by researchers at Memorial Sloan Kettering and NYU Langone suggests that sugar-rich foods may amplify antibiotic-induced disruption of the gut microbiome. The study examined patients’ diets and gut bacteria, alongside controlled experiments in mice. However, the findings do not yet justify advice to cut out sweets whenever you take a routine course of antibiotics.
A Window into a Microbiome Under Siege
The researchers tracked adults undergoing donor stem-cell transplants for blood cancers, recording 9,419 meals during their hospital stays. The microbiome analysis paired dietary records with 1,009 stool samples collected from 158 participants. This meal-by-meal logging reduces the recall errors common in food questionnaires. It also captured the gut ecosystem during a period of extreme upheaval. Stem-cell transplant therapy can involve intensive chemotherapy, radiation, and severe intestinal inflammation.
Patients undergoing stem-cell transplantation typically become poorly nourished during treatment, so they are urged to increase their calorie intake with “sweets.” Typically, they receive prophylactic (preventive) antibiotics. Sugar intake had no measurable effect on gut diversity while patients received these prophylactic drugs. However, when roughly 80% of patients required broad-spectrum antibiotics, such as carbapenems or piperacillin-tazobactam, for suspected infection-related fevers, that changed.
During treatment with these broad-spectrum antibiotics, higher sugar intake was associated with lower microbial diversity and a greater expansion of Enterococcus faecium. This bacterium can cause antibiotic-resistant bloodstream infections in vulnerable patients.
Not Just Candy and Cupcakes
In a hospital transplant ward, “sweets” do not just mean candy bars or cupcakes. The category included sports drinks and commercial liquid nutritional supplements. Such supplements can be vital in preventing malnutrition in people with painful mouth sores, nausea, and loss of appetite.
Both nutritional supplements and other sweets category foods were linked to lower microbial diversity during broad-spectrum antibiotic treatment. Further analysis pointed more strongly toward added sugars than naturally occurring sugars.
The researchers estimated an additional 20.6% reduction in microbial diversity for each 100-gram increase in daily sugar intake during broad-spectrum antibiotic treatment, compared with periods without it. This statistical estimate does not tell us how much sugar, if any, people should cut back on during antibiotic treatment, or what happens after an ordinary serving of dessert.
Separating Sugar's Effects From the Effects of Illness
In observational medical research, correlation does not prove causation. Patients who need broad-spectrum antibiotics are often sicker than those who do not. Could their severe illness itself be driving the microbiome disruption? The researchers addressed this concern in two ways:
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First, their statistical analysis adjusted for treatment intensity and indicators of illness, including painkiller use as an indirect measure of severe mouth and throat sores that can make eating difficult. The association between sugar intake and lower microbial diversity during broad-spectrum antibiotic treatment remained statistically significant. It also persisted in analyses excluding samples collected during treatment for documented infections.
- Second, controlled mouse experiments provided supporting evidence. Healthy mice given a single dose of a broad-spectrum antibiotic had 16-fold higher levels of Enterococcus three days after treatment and 33-fold higher levels after six days when fed sucrose (table sugar), compared with mice receiving the antibiotic alone. The effect persisted even when animals were fed a fiber-free diet, suggesting sugar did more than displace beneficial fiber. Furthermore, adding sucrose not only enlarged the antibiotic-induced bloom — it prolonged the expansion long after the antibiotics were stopped, delaying the gut's natural ecological recovery.
Together, these findings strengthen the case that sugar may interact with antibiotics to amplify microbiome disruption, rather than the association reflecting a sicker patient population.
Sugar, Antibiotics, and a Disrupted Ecosystem
It would be easy to interpret these findings as proof that sugar simply feeds harmful bacteria. The biology, however, appears more complicated.
Most simple sugars are absorbed in the small intestine, but any that remain unabsorbed can reach bacteria in the colon. When researchers colonized mice raised without gut microbes with only Enterococcus and fed them sucrose, the sugar did not significantly increase bacterial levels. This does not rule out sugar acting as a fuel source, but it suggests that the surrounding microbial community also matters.
Antibiotics can disrupt the protective microbial ecosystem that normally keeps potentially harmful organisms in check. Sugar may further alter competition within that ecosystem or affect the body in ways that change the gut environment. The researchers propose several possibilities, but the precise mechanism remains unresolved.
What this means for people taking antibiotics at home
Can we take these findings and tell an otherwise healthy person taking antibiotics for a common infection to skip dessert?
Not yet.
Stem-cell transplant recipients receiving intensive treatment are in a very different situation from someone recovering at home on a short antibiotic course. We cannot assume their microbiomes respond in the same way, nor can we rule out a similar interaction occurring outside hospital settings. Crucially, we do not yet have a trial showing that reducing dietary sugar during a routine antibiotic course speeds gut recovery or lowers the risk of common side effects such as diarrhea.
Good Nutrition Without New Rules
The evidence on sugar restriction during antibiotics is still developing, but eating well remains a practical way to support both yourself and your gut microbes—during antibiotic treatment and generally:
- Keep fiber-rich foods on the menu: Vegetables, pulses, and whole grains provide fuel for gut microbes. A small study in healthy volunteers found better recovery of gut microbial diversity after antibiotics and an osmotic laxative on diets containing fiber than on a fiber-free diet. Keep these foods in your meals as your appetite and digestion allow.
- Enjoy fermented foods: Yogurt, kefir, and fermented vegetables can add variety to your diet. A trial in 36 healthy adults found that increasing fermented foods increased gut microbial diversity, although their role during antibiotic treatment remains uncertain.
- Focus on overall nourishment: If an infection has reduced your appetite, prioritize manageable meals and snacks that provide energy and protein, and keep up your fluid intake.
This study moves the sugar–antibiotic interaction beyond speculation. In transplant patients receiving broad-spectrum antibiotics, higher sugar intake was associated with greater microbiome disruption, while controlled experiments in mice provided evidence of a causal effect.
The findings identify a potentially important interaction that deserves testing in clinical trials. For now, however, they do not justify a new dietary rule to avoid sugar whenever you take antibiotics.
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Angela Dowden
Angela Dowden is a British health journalist, author, and Registered Nutritionist. She has nearly 30 years’ experience bringing food, nutrition, and health science to life for international audiences through her print and online work.
