Neuroscience and biobehavioral reviewsFeb 18, 2026

How Gut Microbiome Diversity May Affect Sleep and Body Clock Disruptions

Circadian Biology Weekly Brief ↗PubMed ↗DOI ↗

Updated Feb 19, 2026

Abstract

A total of 139 studies were reviewed, highlighting the complex relationship between sleep disruption and the gut microbiome.

Sleep and circadian disruption may lead to changes in host metabolism and immune function through gut microbial mechanisms.
Activation of the hypothalamic-pituitary-adrenal axis is associated with disruptions in sleep and gut microbiome health.
Shifts in bile acid metabolism linked to sleep disruption could influence gut microbiome composition.
Inflammation-related changes in the gut microbiome may occur as a result of altered sleep patterns.
Disruption of tryptophan pathways may connect sleep disturbances to microbiome-mediated effects on health.

Simplified

The bidirectional relationship between sleep physiology and the gut microbiome is mediated by overlapping neuroendocrine, immune, and metabolic pathways, though mechanistic evidence, particularly in humans, remains limited. This scoping review, the second in a two-part series, synthesizes preclinical and translational research examining not only gut microbial composition but also biomarkers reflecting host metabolic or functional responses to sleep and circadian disruption. We reviewed 74 preclinical rodent studies and 65 human studies that assessed sleep, gut microbiome outcomes, and at least one biomarker related to hormones, metabolites, neurotransmitters, or inflammation. Across studies, consistent links emerged between sleep and circadian disruption and changes in host homeostasis through microbiome-mediated mechanisms. These include activation of the hypothalamic-pituitary-adrenal axis, altered bile acid metabolism, inflammation-related microbial shifts, and disrupted tryptophan pathways. Together, these findings suggest that altered sleep influences metabolic and immune function via gut microbial signaling pathways. We highlight directions for future mechanistic research, particularly in translational models, to clarify causal pathways and support microbiome-informed strategies for mitigating the health consequences of sleep and circadian disruption.

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How Gut Microbiome Diversity May Affect Sleep and Body Clock Disruptions

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