A spoonful of sugar may help the medicine go down, but according to a striking new study, it may also make the medicine’s unintended damage to the gut much worse. Researchers who followed people being treated for blood cancers found that those who consumed sugary foods and drinks while taking antibiotics experienced a greater loss of gut bacterial diversity than patients who took antibiotics without the extra sugar. The combination was also linked to an increase in Enterococcus, a group of gut microbes that can be resistant to powerful antibiotics and are often associated with stubborn, difficult-to-treat infections, longer hospital stays and higher mortality. The findings, published September 30 in Nature, were led by Jonas Schluter, a microbiologist at NYU Langone Health, and colleagues. The study focused on 173 patients hospitalized in a specialized treatment center to undergo blood-forming stem cell transplants. This is a grueling process, one that combines intensive chemotherapy or radiation with the transfusion of stem cells to rebuild the body’s ability to make blood. Patients in this situation are extremely fragile. Their immune systems are suppressed, infections are a constant threat, and antibiotics are often a lifesaving part of the daily routine. But those same antibiotics cannot tell the difference between harmful pathogens and the beneficial bacteria that live in the gut. They kill broadly, and the consequences can be profound. The gut microbiome helps digest food, synthesize vitamins, train the immune system and crowd out dangerous bacteria. When it is damaged, patients may become more vulnerable to secondary infections, complications and slower recovery. The new research suggests that diet, specifically simple sugars, may be an overlooked factor in how much damage antibiotics do. It also suggests that the familiar comfort of a sweet snack in the hospital, offered with the best intentions, may have a biological cost at a time when the microbial balance in the gut is already precarious. The findings do not prove that sugar causes these changes in humans, and they do not mean that cancer patients should be denied sweet treats. But they open an important conversation about diet as a serious medical variable, not just a source of calories.
Antibiotics and sugar have both been shown individually to affect gut bacteria. Antibiotics kill susceptible bacteria and can create room for hardier species; sugar can feed certain microbes and shift the balance of the community. But the interaction between the two, particularly in people at high risk of infection, was not well understood. The researchers saw an opportunity in a place where patients’ meals are controlled. Over the course of the study, they tracked more than 9,000 meals eaten by 173 people hospitalized for blood-forming stem cell transplants. Unlike typical nutrition studies that rely on people’s sometimes hazy memories of what they ate, the standardized hospital meals allowed the scientists to measure food intake down to the gram. Stool samples provided a detailed readout of each patient’s gut bacteria, which could then be compared with the precise nutrient content of what they had eaten. “Diet records are one of the biggest black boxes in a lot of diet microbiome studies,” says Tiffany Weir, a microbiologist at Colorado State University who was not involved in the research. Here, the black box was opened. For patients, this study happened in the middle of one of the most difficult chapters of their lives. They were not just numbers in a database; they were people enduring isolation, fear and physical strain, and the hospital tray may have been one of the few things they could still control. The fact that researchers were able to extract such clear patterns from those meals is a reminder that the environment around a sick person matters down to the smallest detail. Schluter notes that these patients experience such dramatic shifts in their microbiomes that they offer a unique window into processes that also occur, in less extreme forms, in healthy people. “We believe [these findings] are also relevant in the healthy context,” he says.
The results were sobering. For every additional 100 grams of sugar that patients on antibiotics ate in the two days before a stool sample was taken, researchers observed a 24 percent decrease in bacterial diversity. To put that in perspective, 100 grams of sugar is roughly the amount in 2.5 cans of Coca-Cola. Diversity is not just a technical measure; it is a hallmark of a healthy microbiome. A more diverse microbial community is generally more resilient, better able to resist invasion by pathogens, and more likely to produce beneficial metabolites. When diversity falls, the gut ecosystem becomes fragile. The study also found a particularly alarming pattern: high sugar intake during antibiotic treatment was associated with blooms of Enterococcus. These bacteria are often present in small numbers in a healthy gut, but when the normal microbial community is disrupted, they can multiply rapidly. Enterococcus infections are a serious concern in hospitals because many strains are resistant to commonly used drugs, and they can cause infections in the bloodstream, urinary tract and surgical wounds. For immunocompromised patients, the consequences can be severe, including prolonged hospitalization and even death. Schluter puts it in vivid terms. “Some bacteria, sometimes, survive antibiotics, or perhaps more dangerously, they are resistant to [them],” he says. By providing these surviving and resistant microbes with the “universal resource for life, which is simple sugars, we are exacerbating their dominance. It’s almost like burning down the rainforest with a lot of fire, and then trying to extinguish the flames by putting in more petrol.” The image is deliberately extreme, but it captures a subtle ecological point: antibiotics clear away competitors, and sugar then gives the hardiest survivors exactly what they need to take over. In hospitals, sweet foods and drinks are everywhere: juice cups, gelatin desserts, soda brought by visitors, sweetened yogurt. For sick patients, these are often the easiest things to eat, especially when nausea and pain blunt appetite. The study does not suggest that sugar is evil, but it highlights that nutrient choices can either help or hinder an already stressed microbial community.
To test whether sugar truly helps drive the problem, the researchers turned to mice. They gave mice either a standard diet or a sucrose-rich diet, then exposed them to a single dose of antibiotics. The sugary diet made the effects of antibiotics worse: enterococcal abundance increased far more in the sucrose-fed mice than in the standard-diet mice. This experimental result is important because it helps separate correlation from causation. In the human data, it is possible that sicker patients ate more sweets, or that other factors contributed to the loss of gut bacteria. The mouse experiment shows that sugar itself is enough to amplify a drug’s damage, at least in a controlled setting. The mechanism makes biological sense. Antibiotics remove the microbial species that are sensitive to the drug, leaving a perturbed landscape. The bacteria that survive are often those that have some resistance, either through mutations or genes acquired from other microbes. These survivors must compete for resources, and simple sugars are a fast, easily accessible fuel. In a normal gut, the overall microbial community would rapidly consume those sugars and keep any one species in check. But after antibiotic disruption, Enterococcus is particularly well equipped to exploit them. The sugar acts like a fertilizer for a weed that has just survived a storm. The mouse data do not prove that the same mechanism works in every human, and the study was not designed to test every kind of antibiotic or every kind of sugar. But together with the large human observation, it builds a strong case that dietary sugar is not a passive bystander during antibiotic therapy. The effect was seen with a single dose, suggesting that even short-term exposure to high sugar can matter. Schluter and his colleagues hope to identify why some bacteria have this advantage, whether because of faster growth, metabolic flexibility or something else. This line of research fits a broader ecological view of infectious disease: the microbes that cause infections are not separate invaders but members of an ecosystem that can be shaped by environmental inputs.
The implications could extend beyond cancer wards. Antibiotics are among the most commonly prescribed medications in the world, prescribed for everything from ear infections to pneumonia. Many people have experienced the digestive upset that comes with a course of antibiotics, and for some, the gut community never fully returns to its previous state. If sugar amplifies antibiotic-induced damage, then lowering sugar intake during treatment could be a simple, low-cost way to protect the microbiome. Sarah Berry, a nutrition scientist at King’s College London who was not involved in the study, says, “Reducing sugar intake could be another way for patients to support their gut microbiome during antibiotic treatment.” But she and the researchers stress that more research is needed. This was a specific group of patients with blood cancers, undergoing intense treatment in a hospital. Their immune systems, gut microbiomes and nutritional needs are very different from those of a healthy adult taking a short course of antibiotics. It is not yet clear whether the same pattern would hold in other populations, or whether the effects would be as large. Still, the study fits with a broader body of evidence that diet can shape how the gut responds to stress. Fiber, for example, has been shown to support beneficial bacteria, while highly processed foods and simple sugars often correlate with lower diversity in population studies. For patients in the hospital, dietary changes should be made carefully, with medical guidance, because some patients need extra calories and may have difficulty eating enough. A sweeping call to eliminate sugar from hospital menus could do more harm than good if it makes food unpalatable for people who are already struggling to eat. The goal is not to add another burden to patients but to find ways to make their treatment more supportive. Even in healthy people, antibiotics can cause blooms of Enterococcus; dietary sugar may tip the balance further. Researchers are beginning to think of antibiotics and diet as a combined intervention, not separate concerns.
At its heart, this study is about the hidden consequences of the decisions we make during illness. No one taking antibiotics wants to think about the collateral damage happening inside their body; they just want to get better. But the microbiome is not an optional organ. It is deeply involved in immunity, inflammation and recovery. Schluter emphasizes that antibiotics remain necessary. “You need to take antibiotics to fight infections, but you should also be aware that they have side effects to the microbiome,” he says. “Now, we need to find strategies to mitigate this damage.” The research points toward one such strategy: paying attention to sugar. It may not be realistic, or even desirable, to ask a patient undergoing a stem cell transplant to avoid every dessert. Food is not only fuel; it is comfort, culture and a small source of joy in an otherwise sterile hospital room. But there may be middle paths: swapping a sugary drink for water, opting for a piece of fruit instead of candy, or eating a meal that contains fiber alongside whatever sweetness it includes. These small choices, multiplied over days and weeks, might help protect the trillions of microbes that help keep the body alive. Schluter hopes future clinical trials will test whether sugar reduction, or other dietary changes, can improve patient outcomes. The ultimate goal is not to frighten people away from antibiotics or to make them feel guilty about a cookie. It is to understand, with scientific precision, how to heal the body without sacrificing the invisible ecosystem inside it. In the hospital and at home, the question is no longer just “What medicine should I take?” but “How can I take it in a way that also nourishes the life within?” The humble spoonful of sugar may help the medicine go down, but perhaps the wisest medicine of all includes a spoonful of caution.
