137 Gut Bacteria Species Are Linked to How Well You Sleep, Large Study Finds

Poor sleep and disrupted body clocks are already tied to a long list of chronic diseases, from heart disease to cognitive decline. Now, a large Dutch population study published in Nature Communications suggests the gut microbiome is part of that story in humans, not just in rodents. Analyzing 6,941 participants from the Lifelines cohort, researchers identified 137 bacterial species associated with at least one sleep characteristic, and found that what you eat may be the bridge connecting your gut bugs to when and how well you sleep.

137 Gut Bacterial Species Associated with Sleep Quality, Jet Lag, or Chronotype

Of the 137 species flagged in the analysis, 119 were linked to sleep quality as measured by the Pittsburgh Sleep Quality Index, 20 to social jet lag (the misalignment between your biological clock and your work schedule), and 24 to chronotype (whether you are naturally a morning or evening person). Five species showed up across all three measures: Clostridia unclassified SGB14844, Coprococcus eutactus, Oscillibacter sp. ER4, GGB9615_SGB15053, and Ruminococcaceae unclassified SGB15236. Earlier work had suggested that microbiome diversity improves sleep efficiency, but this study goes further by naming specific species and connecting them to multiple dimensions of sleep at once.

The direction of effect was not uniform within bacterial families. Among Ruminococcaceae, the most represented family with 44 associated species, one strain (GGB9602_SGB15031) pointed toward better sleep while Flavonifractor plautii was linked to poorer sleep. This means family-level microbiome summaries may obscure clinically important variation at the species level.

Daytime sleepiness, measured by the Epworth Sleepiness Scale, was the exception: no individual species reached statistical significance for that trait. The researchers also noted that species associated with beneficial sleep tended to be common, present in more than half of participants, while those tied to poorer sleep were less prevalent.

Sleep Disruption and Gut Dysbiosis Create a Two-Way Health Risk

Among the 6,941 participants, 74.9% were classified as good sleepers and 25.1% as poor or very poor sleepers. Females reported worse sleep quality than males, and older participants experienced less social jet lag, a pattern consistent with age-related shifts in circadian timing. Poor sleep clustered with psychological disorders, gastrointestinal conditions, and Western dietary patterns.

The stakes are not trivial. Sleep disorders that disrupt gut microbiota circadian rhythms can drive chronic inflammation and raise cardiovascular and cerebrovascular disease risk, creating a feedback loop where poor sleep worsens the gut environment, and a disrupted gut environment makes sleep harder to regulate. The Lifelines data add human-scale evidence to what had mostly been a rodent-based story: both alpha diversity (the richness of species within an individual) and beta diversity (differences in composition between people) were significantly associated with sleep quality, social jet lag, and chronotype.

How Diet, Coffee, and Alcohol Connect the Gut to the Body Clock

Diet emerged as one of the strongest mediating variables in the study. A high Healthy Eating Index score, along with higher intake of polysaccharides and proteins, was associated with better sleep metrics. Western diet patterns and higher maltose intake were associated with worse sleep. Higher total caloric intake correlated with increased daytime sleepiness.

Coffee and alcohol showed particularly specific associations. Coffee intake was strongly linked to increased abundance of Clostridium phoceensis and several Lachnospiraceae and Ruminococcaceae strains. More intriguingly, mediation analysis found that two Clostridia species (UC5_1_1E11 and SGB14844) mediated 8.3% of the effect of coffee intake on social jet lag. In the reverse direction, coffee intake mediated 65% of the effect of social jet lag on the abundance of those same two species, suggesting the relationship runs both ways. Alcohol consumption was linked to a later chronotype and to reduced abundance of Clostridium leptum and Coprococcus eutactus.

The researchers used penalized structural equation modeling to untangle these pathways, which is one of the more rigorous approaches available for observational mediation work. Still, the causal arrows remain provisional.

What a Cross-Sectional Design Can and Cannot Tell Us

The study's scale is its primary strength: nearly 7,000 participants, species-level metagenomic sequencing using MetaPhlAn v4.0.6, and a replication cohort of roughly 1,500 people from Lifelines-DEEP, where 35.6% of species associations held up despite methodological differences between the two datasets. Sensitivity analyses adjusting for mental health conditions, gastrointestinal disease, physical activity, alcohol use, and sleep medication use did not substantially change the findings.

The central limitation is one that applies to any cross-sectional study: the observational design makes establishing causality through these cohort analyses genuinely difficult. The study cannot determine whether gut bacteria influence sleep, sleep influences gut bacteria, or both are driven by a third unmeasured factor. Self-reported sleep and diet data add further noise. And because statistical power decreases for rare or low-abundance species, subtle effects in that part of the microbiome may have been missed entirely.

Two Clostridia species flagged in the mediation analysis (UC5_1_1E11 and SGB14844) are poorly characterized, meaning their mechanism of action, whether through circadian-relevant metabolites or some other pathway, remains unknown.

Dietary and Microbiome Interventions as Potential Targets for Better Sleep

The authors suggest that lifestyle changes, particularly dietary shifts, could interrupt the negative feedback cycles linking poor sleep to gut dysbiosis. Reducing coffee and alcohol intake, improving overall diet quality, and potentially using probiotics or prebiotics to modulate specific bacterial species are proposed as public health strategies worth testing in randomized trials.

Five species associated with all three sleep characteristics (quality, jet lag, and chronotype) give researchers a shortlist of targets for future mechanistic work. Whether manipulating their abundance in humans can meaningfully shift sleep outcomes is an open question, but the identification of specific, replicable microbial associations in a cohort of this size makes that next step considerably more tractable than it was before.

Evidence rating

EMERGING — 86/100

Caveats:

• Cross-sectional design: this study shows associations, not cause and effect — it cannot confirm whether gut bacteria drive sleep changes or vice versa.
• Sleep and diet data were self-reported, which introduces the possibility of recall or reporting bias.
• Funding source was not disclosed in the article.
• While findings were partially replicated in an independent cohort, most bacterial species identified are poorly characterized and their functional mechanisms in humans remain speculative.

Large cross-sectional cohort study (n=6,941) using metagenomic sequencing and validated sleep questionnaires. Findings represent associations, not established causal relationships, and the direction of effect between sleep and microbiome composition cannot be determined from this design. Approximately 35.6% of species-level associations were replicated in an independent cohort of ~1,500 participants, though methodological differences between cohorts limit direct comparison.

References

1. Jiafei Wu, Sergio Andreu-Sánchez, Haoran Peng, et al. (2026). The interplay of sleep characteristics with health factors and gut microbiome. Nature Communications. https://doi.org/10.1038/s41467-026-68791-9
2. Robert P. Smith, Cole Easson, Sarah M. Lyle, et al. (2019). Gut microbiome diversity is associated with sleep physiology in humans. PLOS ONE. https://doi.org/10.1371/journal.pone.0222394
3. Monika Sejbuk, Adam Siebieszuk, Anna Maria Witkowska (2024). The Role of Gut Microbiome in Sleep Quality and Health: Dietary Strategies for Microbiota Support. Nutrients. https://doi.org/10.3390/nu16142259
4. Hoon Je Seong, Younghwa Baek, Siwoo Lee, Hee-Jeong Jin (2024). Gut microbiome and metabolic pathways linked to sleep quality. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2024.1418773