The bacteria living in your guts and mouths could be controlling how you sleep at night. Now scientists want to use them to help you rest better.

As you lie in bed tonight, your body will be a teeming mass of activity. Across almost every inch of your body – and inside it too – billions of tiny organisms are writhing and jostling for space. But if that horrifying thought is likely to keep you up at night, consider this: they might also help you get a better night's sleep.

Emerging research suggests that the communities of bacteria, viruses and fungi that make up our body's microbiota can influence our sleep. Depending on the composition of our personal microbial ecosystem, the amount of shut eye we get can either improve or deteriorate.

And tantalisingly, it could offer new ways of tackling sleep-related conditions caused by a disrupted body clock, described by sleep scientists as circadian rhythms. While many people currently rely on sleeping pills to quell persistent insomnia, the future might see friendly bacteria deployed to help us nod off, and even address obstructive sleep apnoea, a condition in which people struggle to breathe normally while asleep. It would bring new meaning to the term "sleep hygiene".

"The predominant theory for a long time has been that having sleep disorders is disruptive to our microbiomes," says Jennifer Martin, a University of California Los Angeles professor and board member of the American Academy of Sleep Medicine. "But some of the evidence we're seeing now indicates that it's probably a relationship that goes in both directions."

In May, new research presented at an academic conference for sleep scientists summed up what a growing number of other studies are revealing. It found that teenagers and young adults with a greater diversity of microbes in their mouths tended to have a longer sleep duration.

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Research has also shown that people with medically diagnosed insomnia have lower bacterial diversity in their guts compared to normal sleepers, something typically linked to a less healthy immune system and impairments in dealing with fats and sugars, which can lead to an increased risk of diabetes, obesity and heart disease. Another study, in which 40 people volunteered to wear sleep trackers for a month and have their gut microbiome analysed, also found that poor sleep quality correlated with a less diverse population of gut microbes.

Plus, people with social jetlag – where their sleep patterns during the working week and weekend vary enormously – had significantly different gut microbiomes to those whose sleep patterns did not vary much, according to data analysed by UK health-tech company Zoe.

"Circadian rhythm disruption occurs in people who stay up later and sleep in on the weekends, those who work long hours, like first responders, police and security, paramedics and the military, and in people who eat too close to bedtime," says Kenneth Wright, a professor of integrative physiology at the University of Colorado Boulder in the US. "This can cause gastrointestinal disturbances and metabolic diseases, which are common for example in shift workers, and a disturbed microbiome may play a role."

It's possible that individuals with disrupted sleep tend to follow less healthy diets, which then impacts their microbiome, suggests Sarah Berry, a nutritional sciences professor at King's College London and chief scientist at Zoe. She cites other research not conducted by Zoe that found that short sleepers tend to subconsciously increase their sugar intake.

"Part of the theory behind this is that when you've had a bad night's sleep, the reward centres in your brain are heightened the next day, and so you seek out that quick fix," she says. "Your brain is kind of tricking you into feeling, 'Ok, I need refined carbohydrates', to get that quick burst of energy."

But changing dietary patterns in response to sleep deprivation is not the whole story. Berry and her colleagues found nine species that were greater in abundance and eight that were less abundant in people with social jet lag compared to those without this variation in sleep patterns. But they found that diet appeared to only account for changes in abundance for four of these microbe species.

Jaime Tartar, a professor of psychology and neuroscience at Nova Southeastern University in Florida who was not involved in the Zoe study, says she has become increasingly convinced that certain microbes play a direct role in sleep. She cites Firmicutes, one of the most dominant taxonomic groups of bacteria found in the gut. In tests where Tartar and her colleagues monitored the sleep and tested the gut microbes of 40 men, they found 15 different groups of Firmicutes bacteria that correlated with a number of sleep metrics in varying ways. "We don't have all the answers right now, but it certainly seems that some can improve sleep and others can impair sleep," she says.

In some cases, sleep disruptions might actively drive shifts in these microbial populations through impairing the immune system and its ability to regulate microbes, which could in turn increase the likelihood of longer-term sleep problems. 

But researchers including Tartar and Martin suggest that some sleep problems could also be initiated by microbial imbalances in the gut or mouth. They believe that certain bacteria may actively alter the quality of the sleep we get by shifting our circadian rhythms – the internal body clock that governs our sleep – and altering our food intake, which also impacts the kip we get.

Some evidence for this comes from a series of studies involving so-called faecal transplants. In one 2024 study, scientists transplanted faeces – along with the gut microbes it contained – from humans and implanted it into the intestines of mice. Rodents who received faeces from people suffering from jetlag and insomnia developed insomnia-like behaviours, becoming more awake during their typical sleeping hours. In another study where mice received a series of gut microbes from humans before, during, and after recovery from jetlag, the transplantation of microbes during the jetlag phase saw them gain weight and struggle to control their blood sugar. 

A number of small-scale studies in humans by researchers in China have shown that faecal transplants could help to improve the sleep of patients suffering from chronic insomnia and sleep disorders. Of course, it's worth remembering that many aspects of sleep involve psychological factors, so it is possible that receiving a transplant led patients to change their mindset in a way that allowed them to sleep more soundly. A randomised, double-blind clinical trial will be needed to test the efficacy properly, the researchers say.

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