Sugary foods combined with antibiotic treatment can damage the gut microbiome in ways that could leave people vulnerable to dangerous infections, a new study shows.

The new research, published in the journal Nature, took advantage of a natural experiment: It looked at what happened to gut bacteria in cancer patients who were hospitalized and treated with sustained antibiotics before receiving stem cell transplants. Because the patients only ate food prepared by the hospital, researchers knew exactly what and how much food they ate – a rarity in nutrition studies, which typically rely on participants to recall what they ate hours or days earlier, something people are notoriously bad at.

The gut microbiome consists of trillions of bacteria, viruses and other microbes that populate human intestines. These tiny organisms perform a host of functions including helping with digestion, making essential vitamins, and playing a role in immune function. Science has shown the microbiome also communicates with the brain to produce neurotransmitters like serotonin, which are important for sleep, mood and stress levels.

Studies have shown that the numbers and variety of bacteria that live in the gut depend largely on diet. People who eat varied, plant-based, fiber-rich diets tend to have higher diversity of organisms in the intestines compared with those who eat diets with more highly processed foods. In general, the more diverse a person’s microbiome is, the healthier it is. A dense, diverse community of bugs in the gut is able to prevent bad actors – called pathobionts – from taking over and causing illness.

“One of the things that that differentiates this study from other ones that have been previously published is that the patients are having their microbiome pummeled, and they’re also having their nutritional state disrupted by the cancer treatment,” said study author Dr. Jonathan Peled, a physician scientist at Memorial Sloan Kettering.

The research, which was led by scientists at Memorial Sloan Kettering Cancer Center and NYU’s Langone Health in New York, and City of Hope Cancer Center in Los Angeles, looked at what happened after antibiotics and hospital food destabilized and disrupted normal gut flora. They used this state of disruption as a window to see the effects of certain types of foods on the composition of the gut microbiome.