Slashing sugar intake before antibiotics may save your microbiome

Avoiding sugary foods while taking a course of antibiotics might help protect the diversity of your gut microbiome.

The array of bacteria in the gut plays a crucial role in supporting our digestion and our physical and mental health. But this diverse community can be disrupted by antibiotics, leading to digestive problems, fatigue and flare-ups of skin conditions. Stopping such disruption is particularly important for people with cancer, because greater gut microbiome diversity has been linked to better survival rates.

To dig into this issue, Jonathan Peled at the Memorial Sloan Kettering Cancer Center in New York and his colleagues have studied 158 people with blood cancers. The participants were hospitalised for several weeks as they had chemotherapy to knock out their immune systems before an infusion of stem cells. To prevent potential infections, each person took at least one type of antibiotic.

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The researchers monitored changes in the participants’ gut microbiomes by analysing stool samples. Crucially, they also knew exactly what people had eaten, and when they had eaten it. Each time a patient ordered a meal from the hospital kitchen, between 12 days before the stem-cell transplant and 49 days after, the food tray arrived with a questionnaire for recording the amount of each item they consumed.

“We were able to collect these frequently and fill in the gaps,” says Peled. “Suppose a patient ate half a lasagna. We know the recipe and the standard serving size and the nutritional information of each ingredient. I think this is the closest anyone has ever come to precisely recording everything that goes in and linking it to what comes out.”

The researchers recorded more than 40,000 food items, creating a dataset with a level of detail that is rarely possible in nutrition research. When they scoured it for patterns, they found that people who consumed more high-sugar foods while taking antibiotics ended up with a less diverse microbiome.

What not to eat

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Having antibiotics in the 48 hours before the collection of a stool sample was linked to a drop in microbiome diversity that varied between people. However, for every 100-gram increase in consumption of food or drink that is high in sugar (equivalent to one large milkshake) during that time, that drop in total bacterial diversity was on average 24 per cent greater.

The combination of a sugary diet and antibiotic treatment also led to increased numbers of Enterococcus faecium bacteria, which can act as pathogens and cause severe hospital-acquired infections.

The sugar in the gut exacerbates problems caused by the antibiotics, says team member Jonas Schluter at NYU Langone Health in New York. By wiping out many gut bacteria, the antibiotics disrupt the balance of the microbiome, leaving a few “last man standing” strains that aren’t necessarily the most beneficial to our health. “They have survived the assault and then we are feeding them with rocket fuel.”

“It makes sense that potential pathogens are boosted by sugar,” says Nicola Segata at the University of Trento in Italy. This could directly favour pathogens that thrive on sugar but might not be able to break down fibre, and also boost them indirectly, because the beneficial bacteria they are competing with aren’t getting the fibre they need to recover from the antibiotic assault, he says.

Experiments in mice backed up the idea that sugar was responsible for boosting potentially pathogenic bacteria. Mice given the antibiotic biapenem while eating a high-sucrose diet had a 16.3-fold increase in the Enterococcus population in their guts by day three and a 33.4-fold boost by day six. Mice that ate the high-sugar diet without antibiotics kept their bacterial diversity.

Peled says they saw similar effects when mice were fed on a commercial fruit smoothie, containing naturally high levels of the sugar fructose.

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The work has implications both inside and outside the hospital. Doctors often recommend smoothies or milkshakes to cancer patients to boost nutritional intake. This recommendation might have to be reevaluated if the patient is also taking antibiotics, says Peled.

Avoiding sugary foods while taking antibiotics could also be relevant to the wider world. “Many of us are motivated to find ways to protect the microbiome when we or our children are prescribed antibiotics. Limiting the intake of sugary foods offers a potential way to do that,” says Peled. “It’s very feasible, likely to be very low toxicity, very tolerable and very economical.”

He points out that standard dietary recommendations involve avoiding excessive sugar intake, so it’s something we should all be trying to do anyway.

A window opens for bacteria to recolonise your gut when antibiotics have disrupted the microbiome there, says Segata, who has shown that infants pick up new strains of bacteria faster after a course of antibiotics. To encourage the return of a wide array of beneficial bacteria, he recommends eating a high diversity of plant-based foods.

Nature DOI: 10.1038/s41586-026-11077-3