Ilia Karatsoreos, an assistant professor in Washington State University, shifted mice from their usual cycle of sleeping and waking and saw that, while they got enough sleep, it was of poorer quality.
The animals also had a disrupted immune response, leaving them more open to illness.
The study is a look into the circadian process, a brain-driven clock that controls the rhythms of various biological processes, from digestion to blood pressure, heart rate to waking and sleeping.
The cycle is found in most everything that lives more than 24 hours, including plants and single-celled organisms.
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Typically, sleep researchers have a hard time studying sleep deprivation and the circadian cycle separately, as a change in one usually affects the other.
However, the researchers saw their model did not affect an animal's total sleep, giving them a unique look into the effects on the timing of the sleeping-waking cycle.
The researchers used mice whose body clocks run at about 24 hours and housed them in a shorter 20-hour day.
The researchers saw that the disrupted animals had blunted immune responses in some cases or an overactive response in others, suggesting the altered circadian cycle made them potentially less able to fight illness and more likely to get sick.
"This represents a very clear dysregulation of the system. The system is not responding in the optimal manner," said Karatsoreos.
Over time, Karatsoreos said, this could have serious consequences for an organism's health.
The mice woke more often and the pattern of electrical activity in their brains related to restorative sleep was greatly reduced.
The study was published in the journal Brain, Behaviour and Immunity.