Sugar and antibiotics may be a worse combination for the gut than doctors realized. A study published online in Nature on Sept. 30, 2026, led by researchers at Memorial Sloan Kettering Cancer Center (MSK), found that hospitalized patients who ate more sugary foods while on antibiotics lost more of their gut-microbiome diversity and saw larger blooms of Enterococcus, a hospital-associated bacterium. Follow-up experiments in mice pointed the same way: added sucrose made antibiotic-driven Enterococcus overgrowth bigger and longer-lasting.
The work comes from a very specific group of patients, people undergoing stem cell (hematopoietic cell) transplants, so it is not proof that a cookie with a course of amoxicillin harms a healthy adult. But it is one of the most detailed looks yet at how specific foods interact with antibiotics inside the gut, and it suggests diet could become a practical lever in hospital care. Here is what the researchers did, what they found, and where the evidence stops.
Key Takeaways
- Who was studied: 173 adult allogeneic stem cell transplant patients at MSK (2017–2022), with 9,419 hospital meals and 1,009 stool samples analyzed.
- Main finding: During antibiotic exposure, every additional 100 grams (dry weight) of sweets was associated with an extra 24.1% drop in gut microbial diversity (95% CI 7.7%–38.1%).
- No effect without antibiotics: Outside antibiotic windows, sweets intake and microbiome diversity were not correlated.
- Mouse confirmation: Sucrose increased antibiotic-driven Enterococcus expansion about 16-fold on day 3 and 33-fold on day 6.
- Big caveat: The human data are observational, not a randomized trial.
What the Sugar and Antibiotics Study Found
Verified findings below come from the peer-reviewed paper, “Sugar-rich foods exacerbate antibiotic-induced microbiome disruption” (Dai, Ballweg, Peled et al., Nature, DOI 10.1038/s41586-026-11077-3).
Diversity loss tracked with sweets, but only on antibiotics
Antibiotics are known to thin out gut bacteria. The team asked whether what patients ate changed how badly. Of nine food groups examined, sweets stood out. In the two days before a stool sample, higher sweets intake during antibiotic exposure predicted lower α-diversity, the standard measure of how many kinds of bacteria are present. When the researchers broke food down by macronutrient, sugar itself was associated with a 20.6% decrease in diversity per 100 grams.
Crucially, the link appeared only when antibiotics were on board. Without antibiotics, the correlation between sweets and diversity was essentially zero (ρ = 0.045, P = 0.28), compared with ρ = −0.195 (P = 3.7 × 10⁻⁵) during antibiotic exposure.
Enterococcus took advantage
Sugar intake during antibiotics was also associated with expansion of Enterococcus faecium, a gut bacterium that can dominate after antibiotics and is linked to bloodstream infections in transplant patients. Each 100 grams of sweets was associated with a 0.89-unit increase in its log-ratio-transformed abundance.
A survival signal, with caveats
Among patients who ate more sugar, each additional day of broad-spectrum antibiotic exposure was associated with higher mortality risk (hazard ratio 1.12; 95% CI 1.01–1.23; P = 0.027). That is an association in a small, very sick population and does not show that sugar caused deaths.
Mouse experiments pointed the same direction
In mice given a single carbapenem antibiotic (biapenem), adding sucrose to drinking water increased Enterococcus burden 16.3-fold on day 3 (P = 0.048) and 33.4-fold on day 6 (P = 0.001) compared with antibiotics alone.
| Measure | Result |
|---|---|
| Patients / meals / stool samples | 173 / 9,419 / 1,009 |
| Diversity change per +100 g sweets (on antibiotics) | −24.1% (95% CI 7.7–38.1%) |
| Diversity change per +100 g sugar (on antibiotics) | −20.6% (95% CI 2–35.6%) |
| Mortality per extra broad-spectrum antibiotic day (high-sugar group) | HR 1.12 (95% CI 1.01–1.23) |
| Mouse Enterococcus increase with sucrose | 16.3× (day 3), 33.4× (day 6) |
Source: Dai et al., Nature (2026). Figures as reported in the paper.
Methodology: How the Researchers Did It
- Precise meal tracking: MSK’s hospital kitchen system recorded each meal served and the percentage eaten (0–100%), creating 9,419 meal records.
- Food classification: Foods were coded with the USDA’s FNDDS system into nine groups and analyzed by dehydrated weight to remove the effect of water content.
- Microbiome sampling: 158 patients had evaluable stool data, a median of five samples each, analyzed by 16S rRNA sequencing.
- Antibiotic exposure: Most patients received prophylactic fluoroquinolones; about 80% also got broad-spectrum drugs such as piperacillin-tazobactam, cefepime, carbapenems, linezolid, metronidazole or oral vancomycin.
- Animal follow-up: Mice received biapenem with or without sucrose to test cause and effect.
Who Is Affected
The most direct relevance is for stem cell transplant and other immunocompromised hospital patients, for whom Enterococcus domination of the gut is a recognized infection risk. Hospital nutrition teams and transplant programs are the likeliest early adopters of any change.
For the wider public, the findings raise a question rather than answer it: whether limiting sugary foods during an ordinary course of antibiotics helps protect the gut. The study did not test that.
Expert Commentary
Senior author Dr. Jonathan Peled of MSK told CNN the effect grew with “the more sugary foods you eat, no matter what type of sugar it is,” with “particularly noxious effects from added sugars.” Dr. Anthony Maresso of Baylor College of Medicine, who was not involved, told CNN the finding matters for transplant recipients because Enterococcus infection is “the number one thing hospitals are worried about.” (CNN via KESQ)
Limitations
- Observational human data: Patients were not randomized to diets, so sicker patients may have eaten differently and also received more antibiotics.
- Narrow population: Transplant patients at one center, nearly all on fluoroquinolone prophylaxis, may not represent outpatients or healthy adults.
- Incomplete diet records: Food brought in from outside the hospital was not fully captured.
- Reverse effects possible: Symptoms such as nausea can change what patients choose to eat.
- Needs replication: The authors call for validation in independent cohorts and, ideally, controlled trials.
Analysis: What Comes Next
Analysis. The obvious next step is a randomized trial testing reduced-sugar diets during antibiotic treatment in high-risk hospital patients. Because hospital menus are already controlled, this is a comparatively low-cost intervention to test. Until then, the study is best read as strong hypothesis-generating evidence. Anyone currently taking antibiotics should follow their clinician’s guidance rather than make major diet changes based on a single study.
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Sources
- Dai A., Ballweg A., Peled J.U. et al. “Sugar-rich foods exacerbate antibiotic-induced microbiome disruption,” Nature, Sept. 30, 2026 (primary source, open access)
- CNN Health (via KESQ): “Eating sugar while taking antibiotics might harm gut bacteria,” Oct. 1, 2026
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