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Shift work affects one in four New Zealanders who make their income by being awake and active when their body would normally be asleep.

Whether it's cleaning offices, driving vehicles, responding to emergencies or guarding warehouses, shift work has been shown to impact the health, social life and sleep quality of workers.

Although scientists are still unclear why working unsociable hours might be related to serious health issues, a new study out this week points towards an unlikely target – the gut.

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Aptly named the graveyard shift, working during the dead hours right before dawn is one of the leading causes of fatigue, which can lead to an increased risk of workplace injury.

However, shift work has also been shown to affect the body in unknown ways increasing the risk of obesity, diabetes, heart disease, stroke and cancer. This correlation between late-night work and medical health is so strong the World Health Organisation has classified shift-work as a probable carcinogen.

We know that our bodies regulate many of our core functions including hormone levels, eating habits, digestion and body temperature through a master clock in the hypothalamus part of the brain.

Called the suprachiasmatic nucleus, it sends signals through the body to keep various processes switched on or off at the right times during a 24-hour day, using daylight as its main cue to stay on track.

Working irregular hours means some shift workers see very little daylight during their waking hours, especially during the winter months, and this can cause confusion with some of these signals.

The new research, published in the Proceedings of the National Academy of Sciences, found that though there is one main biological clock centred in the brain, there are also separate biological clocks within our organs which can respond to sleep disruptions differently.

These peripheral internal clocks constantly try to synchronise based on our activity levels caused by eating meals and exercise.

Using healthy volunteers, the study simulated day shifts or night shifts in the participants, feeding them at the same time intervals and collecting blood samples every three hours.

They analysed levels of hormones in the blood called melatonin and cortisol which are known to rise and fall according to the body's daylight set circadian rhythm.

They also measured metabolites which are the intermediate products caused by the breaking down and digestion of food during metabolism – the process by which the body converts food into energy.

They found that after only three days of following a night shift pattern, the metabolites related to the digestive system had shifted in the volunteers by a full 12 hours aligning with the actual cycle of the volunteer.

This occurred even though the biological clock in their brains had only shifted by 2 hours as the body slowly adjusted to the irregular sleep-wake cycle.

Importantly for disease research, two of the metabolites that changed rhythms in the night shift workers have been associated with chronic kidney disease. As peripheral internal clocks tell the pancreas when to release insulin and the liver when to stop processing glycogen and start metabolising fat, this discovery of signals that are out of sync could help scientists to understand the mechanism behind the increase risk of disease in many shift workers.

Although human bodies have evolved to sleep in the dark, our modern economy keeps going even when the sun goes down.

This research opens up new theories around how behaviour changes such as adjusting meal and sleep times to help to minimise metabolic disruption could be used to survive in a world that needs us to work around the clock.