Antibiotics are among modern medicine’s greatest lifesaving discoveries. They have transformed once-dangerous bacterial infections into treatable conditions and remain indispensable in cancer care, surgery and infectious disease management. But antibiotics come with an unintended consequence: they do not always distinguish between harmful bacteria and the enormous community of beneficial microorganisms living inside our gut.
Recent research suggests that what we eat while taking antibiotics may determine just how badly this microbial ecosystem is disturbed. In particular, sugar-rich foods may worsen antibiotic-induced damage to the gut microbiome.
A study published in Nature examined the relationship between diet, antibiotics and the gut microbiome in patients undergoing allogeneic haematopoietic cell transplantation. The researchers analysed an unusually detailed dataset—9,419 meals consumed by 173 patients, alongside more than 1,000 stool samples from 158 patients.
Their findings point to an important question. Could the food we eat while taking antibiotics influence how quickly our microbial ecosystem recovers?
The invisible ecosystem inside us
The human intestine is home to trillions of microorganisms.
The gut microbiota, comprising bacteria and other microorganisms, constitutes a vital ecology for digestion, metabolism, and immunological control. A population of ‘good bacteria’ alone, however, does not determine a healthy microbiome: other factors like equilibrium, diversity, and the interrelations among myriad microbial species play a major role as well. When this ecological equilibrium is disrupted, it may result in dysbiosis, a condition characterised by reduced microbial diversity and the proliferation of a few other organisms.
Antibiotics are a major cause of such disruption. This is especially evident in patients undergoing intensive medical treatments such as blood or bone-marrow transplantation, where antibiotics may be combined with chemotherapy, radiation and other interventions that further stress the intestinal ecosystem. The new study reveals that diet can become an important additional factor.
A dietary detective story
Studying diet and the microbiome is notoriously difficult. People eat different foods every day, and conventional dietary questionnaires often depend on memory. The researchers overcame some of these limitations by studying patients who were hospitalised for haematopoietic cell transplantation. Because their meals could be recorded repeatedly and stool samples collected over time, the investigators could examine diet and microbiome changes almost day by day.
They recorded thousands of individual meals and classified foods into groups such as grains, vegetables, fruits, meats, milk, oils and sweets. They then compared dietary intake with changes in the gut microbiome.
One pattern stood out. When broad-spectrum antibiotics were being used, higher consumption of sweets and sugars was associated with a sharper decline in microbial diversity.
The researchers estimated that for every additional 100 grams of sweets consumed following broad-spectrum antibiotic exposure, mean microbial diversity decreased by about 24% compared with samples without previous antibiotic exposure. A separate analysis based on macronutrients similarly found an additional decrease of about 20.6% for every 100 grams of sugar. In other words, sugar appeared to act less like an independent villain and more like an amplifier of antibiotic-induced disruption.
The resistant bacterial groups
The most intriguing finding involved Enterococcus, particularly Enterococcus faecium.
Under normal conditions, the gastrointestinal tract harbours a diverse microbial consortium in which many organisms vie for resources and ecological niches. Many of these competitors can be killed or inhibited by antibiotics, allowing only more resistant or adaptable organisms to survive. Enterococcus is one such organism. It can become an important cause of antibiotic-resistant bloodstream infections and has been associated with adverse outcomes in patients undergoing haematopoietic cell transplantation. The study showed that higher sweet intake during antibiotic exposure was associated with increased E. faecium abundance.
The researchers also tested their hypothesis in mouse models. When mice were fed sucrose along with an antibiotic, the Enterococci population increased 16.3-fold on day three and 33.4-fold on day six, compared with antibiotic treatment without additional sucrose. In cultures with only sucrose, enterococcal levels did not increase. This indicates that sugar alone has no effect without antibiotics; the problem arises when antibiotics disturb the gut ecosystem.
The study also showed that this disturbance did not take place due to low fibre intake.
Should we avoid sugar with antibiotics?
Not really. Though the study signals a warning, it doesn’t provide concrete evidence that everyone taking antibiotics will experience the same effect. The human participants in the study were seriously ill patients undergoing intensive cancer treatment, not healthy adults taking a short course of antibiotics for a routine infection.
The researchers themselves point out several limitations. Almost all patients initially received prophylactic antibiotics, while broader-spectrum antibiotics were introduced when clinically indicated. The need for these antibiotics could itself reflect greater illness severity. Dietary information outside hospital-provided food was also incomplete, and treatment-related symptoms could influence what patients chose to eat.
Therefore, the findings should not be interpreted as a reason to discontinue medically necessary antibiotics—or to impose restrictive diets on vulnerable patients without medical supervision. Instead, they open an intriguing area for further research.
Rethinking antibiotic prescriptions
When doctors prescribe an antibiotic, the prescription traditionally focuses on the drug: which antibiotic, what dose and for how long. Emerging microbiome science suggests we may eventually need to think more broadly. Perhaps an antibiotic prescription could one day include advice on how to protect the microbial ecosystem during treatment.
The new Nature study suggests that temporarily reducing foods rich in simple sugars could be one possible strategy. But prospective clinical trials must demonstrate whether this actually improves patient outcomes. The authors explicitly call for such studies.
The larger lesson extends beyond sugar. Our gut is an ecosystem, not merely a digestive tube. Medicines, food and microbes constantly interact within it. An antibiotic may be prescribed to eliminate an infection, but it inevitably changes the microbial environment in which thousands of other organisms live.
The emerging challenge for medicine is therefore not simply how to kill harmful bacteria, but how to do so while preserving the microbial communities that help keep us healthy. And sometimes, the difference may lie not only in the medicine we take—but also in what we put on our plate while taking it.
(Dr.Biju Dharmapalan is an adjunct faculty member at the National Institute of Advanced Studies, IISc campus, Bengaluru, and dean, academic affairs, Garden City University, Bengaluru. bijudharmapalan@gmail.com)