
There’s a lot of discussion these days about 
gut health (link is external)—how a healthy gut can support overall 
health,
 and the ways a compromised gut may contribute to illness and disease. 
We’re learning more about the complexity of the vast, dense, microbial 
world of the human gut and its influence over immune health, hormone 
balance, 
brain function, and mental and physical equilibrium. What relationship exists between 
sleep
 and this microbial ecosystem within the body? Emerging science 
demonstrates that there is a very real and dynamic connection between 
the microbiome and sleep itself.
What is the microbiome?
The term 
microbiome (link is external)
 can mean a couple of different things. It is sometimes used to describe
 the collection of all microbes in a particular community. In scientific
 terms, the microbiome can also refer to the 
genes
 belonging to all the microbes living in a community. The microbiome is 
often seen as a genetic counterpart to the human genome. 
The genes that make up a person’s microbiome are far more numerous 
than human genes themselves—there are roughly 100 times more genes in 
the 
human microbiome (link is external)
 than in the human genome. This makes sense when you consider that there
 are somewhere in the neighborhood of 100 trillion microbes living in 
(and on) each of us—a combination of many different types, including 
bacteria, fungi, viruses and other tiny organisms.
This vast array of microbial life lives on our skin and throughout 
the body. The largest single collection of microbes resides in the 
intestine—hence the attention to “gut” health. Here, trillions of 
microscopic organisms live and die—and appear to exert a profound effect
 on human health.
The microbiome and sleep
The human microbiota is a complicated, dynamic ecosystem within the 
body. It appears to interact in some important ways with another 
fundamental aspect of living—sleep. As with much about the microbiome, 
there is a tremendous amount we don’t know about this interaction. That 
said, there are some fascinating possible connections and shared 
influences. Scientists investigating the relationship between sleep and 
the microbiome are finding that this ecosystem may affect sleep and 
sleep-related physiological functions in a number of ways—shifting 
circadian rhythms (link is external), altering the body’s 
sleep-wake cycle (link is external), and affecting 
hormones that regulate sleep (link is external) and wakefulness. Our sleep, in turn, may affect the health and diversity of the human microbiome.
The microbial life within our bodies is in perpetual flux, with 
microbes constantly being generated and dying. Some of this decay and 
renewal naturally occurs during sleep. There’s no answer yet, however, 
to the important question: What role does sleep itself play in 
maintaining the health of the microbial world inside us, and which 
appears to contribute so significantly to our health?
There are some important signs of a significant connection: We’ve seen research demonstrating that 
circadian rhythm disruptions (link is external) can have negative effects on gut microbiota. (
More on this shortly.) There’s also evidence that the disordered breathing associated with 
obstructive sleep apnea (OSA) (link is external), a common 
sleep disorder,
 may disrupt the health of the microbiome. Scientists put mice through a
 pattern of disrupted breathing that mimicked the effects of OSA, and 
found that the mice that lived with periods of OSA-like breathing for 
six weeks showed significant changes to the diversity and makeup of 
their microbiota.
Sleep and the gut-brain connection
A significant, fast-growing body of research illustrates the far-reaching effects of the 
microbiome (link is external)
 over brain function and brain health—as well as the influence of the 
brain over gut health and the microbiome. This “gut-brain axis” appears 
likely to have a profound influence over nearly every aspect of human 
health and physiological function, including 
sleep (link is external).
The constant communication and interplay between the gut and the 
brain has the potential to influence and intersect with sleep directly 
and indirectly. Let’s take a closer look at the ways that might occur:
Mood. Studies indicate that the health and balance of the 
gut microbiota (link is external)
 has a significant influence over our mood and emotional equilibrium. 
Disruptions and an imbalance of gut microbes have been strongly 
connected to 
anxiety and depression (link is external). This has potentially significant implications for sleep, as both 
anxiety and 
depression can trigger or exacerbate 
sleep disruptions (link is external).
Stress. Research is also revealing a complicated, two-way relationship between 
stress and gut health (link is external) that also may exert influence over sleep and sleep architecture. Stress is an extremely common obstacle to healthy, 
sufficient sleep (link is external).
Pain. Studies link gut health to pain perception, specifically for visceral pain. An 
unhealthy microbiome (link is external)
 appears to increase sensitivity to this form of pain. Like so many 
others, this connection travels the communication pathway between the 
gut and the brain. The connection between 
sleep and physical pain (link is external) or discomfort is significant—the presence of pain can make falling asleep and staying asleep much more difficult.
Hormones.
 Several hormones and neurotransmitters that play important roles in 
sleep also have significant influence over gut health and function. The 
intestinal microbiome produces and releases many of the same 
neurotransmitters (link is external)—
dopamine, serotonin, and GABA among them—that help to regulate mood, and also help to promote sleep. Also:
- Melatonin, the “darkness hormone" essential to sleep and a 
healthy sleep-wake cycle, also contributes to maintaining gut health. 
Deficiencies in melatonin have been linked to increased permeability of 
the gut—the so-called "leaky gut" (link is external)
 increasingly associated with a range of diseases. Melatonin is produced
 in the gut as well as the brain, and evidence suggests that intestinal melatonin (link is external) may operate on a different cyclical rhythm than the pineal melatonin generated in the brain.
 
- Cortisol is another hormone critical to the human sleep-wake cycle (link is external).
 Rising levels of the hormone very early in the day help to promote 
alertness, focus, and energy. Cortisol levels are influenced in several 
ways within gut-brain axis (link is external):
 The hormone is central to the stress and inflammatory response, and 
also exerts an effect on gut permeability and microbial diversity. The 
changes to cortisol that occur amid the interplay of the gut and brain 
are likely to have an effect on sleep.
 
‘Circadian rhythms’ of the gut?
There is some pretty fascinating research connecting the gut microbiome to 
circadian rhythms (link is external),
 the 24-hour biological rhythms that regulate our sleep and wake cycles,
 in addition to many other important physiological processes. A growing 
number of studies now suggest that the vast and diverse microbial 
ecosystem of the gut has its own daily rhythms. These microbiome rhythms
 appear to be deeply entwined with 
circadian rhythms (link is external)—research suggests that both 
circadian and microbial rhythms  (link is external)are capable of influencing and disrupting the other, with consequences for 
health and sleep (link is external).
The 
rhythms of gut microbes (link is external) are affected by 
diet,
 both the timing of our eating and the composition of the foods we 
consume. A recent study found that mice eating a healthy diet generated 
more beneficial gut microbes, and that the collective activity of 
microbial life in the gut followed a daily—or diurnal—rhythm. That 
rhythm, in turn, supported circadian rhythms in the animal. Mice fed a 
high-fat, stereotypically “Western” diet, on the other hand, produced 
less
 optimal microbial life. The gut microbes of these mice did not adhere 
to a daily rhythm themselves, and also sent signals that disrupted 
circadian rhythms. These mice gained weight and became obese, while the 
mice that ate healthfully did not.
Scientists bred a third group of mice without any gut microbes at 
all. These mice had no signals to send from a gut microbiome. Circadian 
disruption occurred in these mice—but they did not gain weight or suffer
 metabolic disruption, even when fed the high-fat diet. This suggests a 
couple of important conclusions. First, that microbial activity is key 
to normal circadian function—and therefore to sleep. Second, that the 
microbiome is a key player along with diet in the regulation of weight 
and metabolism.
Circadian rhythms and microbiome: A two-way street
Research in humans has returned similar results: The human microbiome
 appears to follow daily rhythms influenced by timing of eating and the 
types of foods consumed, and to exert effects over circadian rhythms. 
Research has also found that the relationship between these different 
biological rhythms works both ways. Scientists have discovered that 
disruptions to circadian rhythms (link is external)—the kind that occurs through 
jet lag,
 whether through actual travel or from “social” jet lag—disrupts 
microbial rhythms and the health of the microbial ecosystem. People who 
experience these changes to microbial rhythms as a result of circadian 
disruption suffer metabolic imbalance, glucose intolerance, and weight 
gain, according to research. And there’s preliminary evidence suggesting
 that 
gender
 may play some role in the relationship of gut microbial health, 
metabolism, and circadian function: a study using mice found that 
females had more pronounced 
microbiome rhythms (link is external) than males.
New understanding of circadian role in metabolism?
We’ve known for some time about the relationship of 
sleep, circadian rhythms, and metabolic health (link is external). Disrupted sleep and misaligned circadian rhythms have been strongly tied to higher rates of 
obesity and to metabolic disorders including
Type 2 diabetes. Our emerging knowledge of the microbiome and its 
relationship to circadian function may in time deliver a deeper 
understanding of how health is influenced by sleep and circadian 
activity.
Science has really only just begun to delve into the world of the 
microbiome and its relationship to sleep as well as health more broadly.
 All the early signs suggest that this is a profoundly important area of
 research; it will be fascinating to see where this takes us, and what 
it means for sleep.