Working night shifts can mess up the body’s natural rhythms so much that the brain and digestive system end up completely out of kilter with one another, scientists say.

Three night shifts in a row had little impact on the body’s master clock in the brain, researchers found, but it played havoc with gut function, throwing the natural cycle out by a full 12 hours.

The finding highlights the dramatic impact that night shifts can have on the different clocks that govern the natural rhythms of organs and systems throughout the human body.

Internal disagreements over night and day may explain why people on night shifts, and those with jet lag, can suffer stomach pains and other gut problems, which clear up once their body has had time to adjust.

“One of the first symptoms people experience when traveling across time zones is gastrointestinal discomfort and that’s because you knock their gut out of sync from their central biological clock,” said Hans Van Dongen, director of the Sleep and Performance Research Center at Washington State University.

For the study, Van Dongen invited 14 healthy volunteers aged 22 to 34 into his sleep lab and split them into two groups. The first spent three days on a simulated day shift and could sleep from 10pm to 6am each night. Those in the second group stayed awake for three nights in a row and were only allowed to sleep from 10am to 6pm.

Over the next 24 hours, scientists took the volunteers’ blood every three hours and sent the samples to the University of Surrey for analysis. There, researchers measured levels of hormones called melatonin and cortisol, which rise and fall according to the body’s master clock, along with levels of metabolites linked to digestion.

The results showed that three night shifts in a row moved the brain’s master clock by about two hours on average. But the impact on the digestive system’s clock was profound, with the stint of night shifts knocking it out by 12 hours.

Our bodies have a central master clock in the brain that draws on changes in ambient light to control when we wake up and when we fall asleep. But many other organs in the body have their own biological clocks, including the digestive system.

“When we looked at the data we saw the massive twelve hour shifts,” said Van Dongen. “We were like, ‘wow, we did not see that coming’.” The night shifts also disrupted the rhythms of two metabolites linked to chronic kidney disease.

Debra Skene, the first author on the study and professor of neuroendocrinology at the University of Surrey, said the findings will help scientists to learn more about the harms that shift work can cause. Previous research has linked shift work to obesity, diabetes and other metabolic disorders that can raise the risk of heart disease, stroke and cancer.

“Now that we know this, we can begin to design studies to see if we can minimise the detrimental effect of mistimed sleep and meals,” Skene said. The study is published in Proceedings of the National Academy of Sciences.

While scientists knew that the biological clocks in organs could fall out of sync with the master clock in the brain, what was striking was by how much. “This study has given us an idea of the scale at which this happens,” said Aarti Jagannath, professor of circadian biology at the University of Oxford, who added that more work was needed to confirm the results.

“What this suggests is that we might be able to use this to tailor meal times to minimise the impact of shift work on health,” she added. “We have followed the light-dark cycle throughout the course of our evolution. But nowadays we can do anything we like at any time of day, so we are giving our body clock very confusing time cues.”