Tossing and turning all night, staring at the ceiling, waiting for sleep to take you to dreamland — yet it never comes? What if your sleepless nights aren’t just stress or late-night scrolling, but the result of a hidden cause of sleepless night that science is only now beginning to uncover?
You see, scientific research is showing something remarkable: the microbes in your gut don’t just help digest food — they can influence your sleep patterns and circadian rhythm.
In some cases, gut bacteria even send signals to your brain that could keep you awake at night, potentially contributing to insomnia and sleep disturbances.
The Gut‑Brain Axis And Sleep
Your gut and brain communicate through a network called the gut‑brain axis, which uses nerves, hormones, and chemical signals to send messages back and forth.
Most importantly, microbes in the gut can produce neurotransmitters and metabolites — like short‑chain fatty acids (SCFAs) — that influence brain chemistry and behaviour.
Rhythms Of Gut Bacteria And Circadian Regulation
A review in Nature Reviews Gastroenterology & Hepatology explains how gut microbes exhibit diurnal oscillations — changes over the day — that help regulate the host’s circadian system:
Certain members of the gut microbiota exhibit diurnal variations in relative abundance and function… these microbial oscillators can modulate host metabolism and rhythm functions by providing input to both central and peripheral circadian clocks.
— Gut microbiota as a transducer of dietary cues to regulate host circadian rhythms and metabolism, Nature Reviews Gastroenterology & Hepatology (1)
This suggests that when these microbial rhythms are disrupted — through poor diet, irregular eating times or stress — they can interfere with your body’s internal clock and sleep‑wake cycle.
How Sleep And Gut Microbes Affect Each Other
Research has also shown direct effects of sleep patterns on the gut microbiota. In a PubMed‑indexed study, sleep deprivation changed the richness and rhythms of gut bacteria in mice:
Sleep deprivation disrupted the diurnal rhythmicity of gut microbiota and blood inflammatory cytokines.”
— Sleep deprivation disrupts diurnal rhythmicity of gut microbiota, (2)
Basically, this supports the idea that poor sleep doesn’t just feel bad — it may actually alter your gut microbial ecosystem, which in turn can affect your metabolism and inflammatory signalling.
Microbiome And Human Sleep Quality
Interestingly, human studies are also beginning to reveal direct links between gut microbiome composition and sleep quality.
A 2025 Scientific Reports study says gut microbial patterns are linked to sleep rhythm development:
The relative abundance of bacterial taxa exhibited rhythmic patterns… demonstrating a significant relationship between gut microbiota rhythms and sleep‑wake cycles during infancy.”
— Linking gut microbiota rhythmicity to circadian maturation in infants, Scientific Reports (3)
Also, a 2024 PubMed study found specific gut microbes and metabolic pathways correlated with sleep scores in adults:
Functional metabolic pathway profiles revealed significant linear correlations… Faecalibacterium prausnitzii showed differences between sleep quality groups and a linear association with sleep quality scores.
— Gut microbiome and metabolic pathways linked to sleep quality. (4)
Basically, this means that not only do gut bacteria fluctuate with your daily rhythm, but their composition and functions has a link with how well you sleep.
Could this be another major reason science refers to your gut as your second brain?
Bidirectional Effects: Gut Bacteria And Sleep Traits
A Mendelian randomisation analysis (a method that uses genetic data to infer causality) found evidence that gut microbiota composition and sleep traits influence each other:
The genetic forecasts of relative abundance of 42 bacterial genera had causal effects on sleep‑associated traits… and sleep‑associated traits also had a causal effect on 39 bacterial genera.
— Associations between gut microbiota and sleep: a bidirectional Mendelian randomisation study. (5)
This suggests a two‑way relationship: your gut bacteria can impact your sleep, and your sleep patterns can change the microbiome.
What This Means For Your Sleep
Taken together, these findings suggest that:
- Gut microbial rhythms help entrain your circadian clock and sleep habits (6).
- Disrupted sleep can, in turn, alter gut bacterial rhythms and composition (7).
- Specific microbes and their metabolites are linked to sleep quality in humans (8).
- There may be reciprocal causal relationships between gut bacteria and sleep traits (9).
How To Support Better Sleep Through Gut Health
While the science is still emerging, current evidence points to several practical approaches:
1. Eat A Diverse, High‑Fibre Diet
A plant‑rich diet supports microbial diversity, which correlates with healthier circadian patterns.
2. Include Probiotics And Fermented Foods
Foods like yoghurt, kefir, sauerkraut and kimchi may help maintain bacteria linked to sleep‑supportive metabolic pathways.
3. Regular Meal And Sleep Timing
Consistent eating and sleeping schedules can help align microbial rhythms with your circadian clock.
4. Manage Sleep And Stress
Good sleep hygiene and stress reduction may protect both your sleep and your gut microbiome.
Final Thoughts
The connection between your gut bacteria and sleep is more than anecdotal — it’s rooted in emerging scientific research.
Your microbiome doesn’t just help digest food — it may also help regulate your body’s internal clock.
Also, it may influence how well you sleep.
As research grows, this could open doors to new sleep‑support strategies based on diet, lifestyle and microbiome‑targeted therapies.