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Snug with your bugs? How microbes control your sleep

The super slot gratisbacteria 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.

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.

But there are other reasons to think it might work. Diet, for example, is well known to affect sleep. When a group of 15 healthy young men followed a high fat, high sugar diet for a week, this altered their brains' electrical patterns during deep sleep, although it's hard to draw firm conclusions from such a small sample size. Similarly, in an experiment where volunteers had their sleep assessed after receiving antibiotics, evidence suggested that this reduced the amount of non-rapid eye movement sleep, an essential part of the sleep cycle where our bodies undergo repairs and new memories and skills are reinforced, although the findings did not apply for all antibiotics, and once again, the study was small.

Changes in the balance of our gut microbes may also alter the amounts of useful chemicals they produce as they help to break down our food. This in turn can influence sleep quality, says Tartar.

We know, for example that some gut microbes produce neurotransmitters such as gamma-aminobutyric, dopamine, norepinephrine and serotonin, or short-chain fatty acids such as butyrate, all of which play a role in sleep. "While they're produced in the gut, they can influence [the] brain," says Tartar.

If those microbes decrease in abundance, then their chemical influence on the brain will likely also lessen while other microbes that use foods such as saturated fat and sugar to synthesise inflammatory molecules can proliferate. Some of these inflammatory chemicals, including certain bile acids, are thought to be capable of disrupting the brain's circadian rhythms.

Martin says the same is likely to be true of the oral microbiome. Heightened inflammation, caused by microbes flourishing in people who have poor diets or poor dental health, could raise those individuals' risk of issues including obstructive sleep apnoea, in which the walls of the throat relax during sleep, interrupting normal breathing.

"If the microbiome is unbalanced, that could lead to local and systemic inflammation that can cause narrowing of the airway, the release of stress hormones and a lot of things that are then disruptive to sleep down the line," says Martin. Narrowed or blocked airways can lead to obstructive sleep apnoea and snoring.

With all of this in mind, it's possible that probiotics (pills that administer a targeted bacterial strain) or prebiotics (non-digestible food ingredients that selectively feed beneficial gut bacteria) could help to treat certain sleep disturbances. Tartar points to one study that showed how a particular probiotic, the Lactobacillus casei strain Shirota, improved sleep compared to a placebo in a group of 94 medical students while they were going through a stressful period in the academic year.

Berry says that Zoe recently completed a six week trial involving 399 healthy UK adults in a project called the BIOME study. The research, which is still undergoing peer review, saw participants receive one of three foods. One group were given a "super fuel for the microbiome" – a prebiotic blend containing more than 30 different whole food ingredients from baobab fruit to lions mane. Another group received a daily probiotic in the form of the bacteria L. rhamnosus. The final group were given?bread croutons with the equivalent calories to the prebiotic blend as a control. Compared to the crouton group, a greater proportion of those receiving the prebiotic blend experienced improved sleep, although this was based on self-reports rather than objective measurements.

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Martin, while intrigued by such results, emphasises the need for larger, more robust trials that compare prebiotic or probiotic interventions to existing treatments, which are already known to be effective for tackling sleep problems. That includes cognitive behavioural therapy (a type of talk therapy often reffered to as CBT) and various medications.

"I'm always cautious about suggesting that someone go spend $30 (￡22) at a health food store on something that doesn't have proven effectiveness, when we know there are effective medical therapies out there," she says.

She expresses interest in finding out whether probiotics could help people with mild cases of obstructive sleep apnoea, possibly in combination with existing oral devices that reposition the jaw in order to help prevent breathing disturbances. Since 20-30% of people with chronic insomnia do not currently respond to cognitive behavioural therapy, Martin wonders if probiotics or prebiotics could help them.

"I would love to see studies like that," she says. "Clinically, we struggle with how to help that subset of patients, a lot of whom don't want to use a sedating medication."

But if microbiology does prove to have a verifiable impact on sleep quality, that could help all kinds of people.

"Circadian disruption is very common in society," says Wright. "It can occur with jetlag, certain careers and lifestyles and age-related diseases. There is the potential for many people to benefit."

It would certainly put a new spin on bed bugs.

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