Microbiota-gut-brain axis pathogenesis and targeted therapeutics in sleep disorders

Sleep constitutes an essential and intricate physiological process that is fundamental to the maintenance of both physical and mental wellbeing. Over the past decade, our understanding of the sleep-control mechanism has advanced rapidly, and substantial progress has also been made in elucidating the interactions between sleep and other biological processes (1, 2). Insomnia is remarkably common in clinical settings, affecting nearly half of all primary care patients (1). It can manifest either in isolation or as a comorbidity with other medical and psychiatric disorders; if left untreated, insomnia may exacerbate the risk of developing or worsening these concomitant conditions (3, 4). In the elderly population, insomnia is frequently associated with comorbidities such as dementia, depression, anxiety disorders, and chronic pain, further complicating its clinical management (5).

Early research on sleep mechanisms primarily focused on the central nervous system (CNS) regulation of sleep–wake cycles (6). The hypothalamic–pituitary–adrenal (HPA) axis, a core regulatory pathway, precisely modulates sleep architecture: morning cortisol peaks facilitate awakening, whereas nocturnal declines support deep sleep. Cortisol follows a 24-h circadian rhythm, playing a critical role in aligning physiological systems with behavioral cycles (7, 8). Notably, sleep disturbances and stress exposure interact bidirectionally. Chronic stress can hyperactivate the HPA axis, elevating nocturnal cortisol levels and thereby impairing sleep initiation and depth. Conversely, recurrent sleep disruption diminishes HPA axis regulatory capacity, increasing vulnerability to stress and establishing a persistent dynamic feedback loop between stress and sleep quality (9, 10). However, recent studies found that central regulatory mechanisms alone cannot fully account for the complexity of sleep homeostasis. For instance, why recovery sleep following deprivation preferentially enhances deep sleep rather than merely extending total sleep time (11), and why sleep disturbances are strongly associated with systemic conditions such as cardiovascular and metabolic diseases (12) and cognitive decline (13). These observations suggest that sleep regulation is not solely a "central" process, but rather requires the coordinated involvement of peripheral organs. Against this backdrop, increasing evidence indicates that peripheral systems, particularly the gut, play a critical role in modulating sleep physiology. Within the research framework examining central-peripheral interactions, the microbiota-gut-brain axis (MGBA) has emerged as a key mechanistic bridge linking these two domains.

Gut microbes can synthesize or modulate neurotransmitters such as γ-aminobutyric acid (GABA), serotonin (5-HT), and dopamine, directly influencing neural circuits that govern sleep–wake balance (14). In addition, gut-derived inflammatory signals-such as lipopolysaccharide (LPS) and pro-inflammatory cytokines including interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and interleukin-1β (IL-1β) can disrupt blood–brain barrier (BBB) integrity, activate microglia, and provoke neuroinflammation, contributing to sleep disturbances (15). The HPA axis, in turn, links sleep stress with microbial dysbiosis: elevating cortisol levels, enhancing gut permeability and reducing mucin production, weakening intestinal barrier integrity and amplifying immune activation. These feedback loops underscore the bidirectional and self-reinforcing cycle between the gut and the brain in sleep disorders (16, 17). Additionally, sleep itself modulates gut physiology. Experimental models demonstrate that chronic sleep restriction disrupts tight junction proteins (occludin, claudin-1), reduces mucosal mucus secretion, alters enteric nervous system excitability, and accelerates intestinal permeability. These effects compromise microbial habitat stability, leading to dysbiosis that perpetuates inflammatory signaling and sleep fragmentation. Together, these pathways illustrate the integrative and bidirectional role of the MGBA in sleep regulation (Figure 1).

Aging further modulates the MGBA-sleep interplay, rendering older adults a high-risk population for sleep disorders. Epidemiological data indicate that the prevalence of insomnia is significantly higher in older adults compared with younger populations, with approximately 41–48% of individuals over 60 years experiencing difficulties initiating sleep, shallow sleep, or sleep fragmentation (18, 19). These phenomena are closely linked to age-related dysregulation of MGBA function. At the level of gut microbiota (GM), characteristic alterations occur in the elderly: on one hand, the abundance of potentially beneficial bacteria, such as faecalibacterium prausnitzii, decreases, while the abundance of pathogenic bacteria increases (20); on the other hand, low-grade inflammation driven by increased pro-inflammatory bacteria can transmit inflammatory mediators to the CNS via the bloodstream, leading to difficulties in sleep initiation and reduced sleep depth (21, 22). Conversely, impaired sleep quality in older adults further exacerbates GM dysbiosis, creating a vicious cycle (23).

This review aims to synthesize current evidence on the MGBA's role in sleep disorders, from mechanistic foundations to clinical translation. Tracing the evolution of MGBA research helps contextualize its growing relevance in sleep medicine. Epidemiological and clinical evidence increasingly links gut dysbiosis to sleep abnormalities, influenced by stress, and circadian rhythms. A thorough understanding of these foundational aspects is crucial for developing novel diagnostic and therapeutic strategies aimed at modulating the MGBA to improve sleep health.

Research on the MGBA has increasingly focused on its role in the pathophysiology of sleep disorders. This bidirectional communication network connects the gut with the CNS, with the GM playing a central role in this dialogue, thereby modulating numerous physiological processes, including sleep regulation. Evidence suggests a reciprocal relationship within this communication: alterations in GM may affect sleep architecture, while sleep disruptions can induce alterations in the microbial community structure (24). Washed microbiota transplantation represents a promising therapeutic strategy, demonstrating efficacy in significantly enhancing sleep quality among individuals with sleep disorders. Washed microbiota transplantation not only shortens sleep latency and prolongs sleep duration but also improves overall quality of life by restoring dysregulated GM homeostasis (25). This suggests that microbiota-targeted therapies could be effective in managing sleep disorders by reestablishing microbial equilibrium.

Beyond sleep-specific implications, the MGBA also intersects with broader health conditions such as metabolic syndrome. As a key communication pathway, the MGBA integrates gut microbial signals with central sleep regulation. Recent studies have identified shared pathological biomarkers and mechanistic overlaps between sleep disturbances and metabolic syndrome within this axis (26). Additionally, beyond metabolic interactions, the bidirectional interaction between GM and the nervous system plays a vital role in maintaining homeostasis. Intestinal dysbiosis has been associated with the onset and progression of various neurological disorders, including Alzheimer's and Parkinson's diseases. By modulating the production and release of neurotransmitters, the GM significantly affects CNS function, thereby establishing a strong rationale for microbiota-targeted interventions in the management of neurological disorders (27). Emerging evidence implicates the MGBA in the pathogenesis of sleep deprivation-induced cognitive impairment. Specifically, chronic sleep loss induces intestinal dysbiosis and promotes activation of the NOD-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome within both colonic and cerebral tissues, ultimately contributing to cognitive deficits. Targeting the NLRP3 inflammasome within the MGBA could offer therapeutic strategies for cognitive impairment associated with sleep disorders (15).

In conclusion, the MGBA is a critical component in understanding and treating sleep disorders. A deeper investigation into the complex bidirectional interplay between the GM and CNS signaling paves the way for novel therapeutic strategies that target the root etiology of sleep disturbances, thereby enhancing patient wellbeing and long-term health. The following sections will elaborate on the central pathological mechanisms by which dysregulated microbial metabolites, immune-mediated inflammation activation, neuroendocrine disturbances, and aberrant vagal nerve signaling contribute to sleep disorders within the MGBA framework.

The MGBA constitutes a dynamic bidirectional network that connects intestinal microorganisms with the central nervous system. Within this framework, several interrelated mechanisms, such as neurotransmitter regulation, neuroimmune interaction, neuroendocrine control, and microbial metabolite signaling, work together to sustain sleep–wake homeostasis. Disturbance of this delicate equilibrium contributes to the development and maintenance of sleep disorders.

Accumulating evidence suggests the pivotal involvement of the MGBA in the pathogenesis of sleep disorders, providing a solid mechanistic basis for targeted therapeutic exploration. Collectively, this body of work suggests a bidirectional pathological cycle between the MGBA and sleep regulation: gut dysbiosis impairs microbial metabolite signaling and promotes neuroinflammation, thereby disrupting sleep, whereas sleep deprivation further aggravates dysbiosis by altering gut motility, permeability, and immune balance (65, 66). Microbial-derived metabolites, such as tryptophan derivatives and phenethylamine, can promote melatonin synthesis and influence sleep–wake regulation, underscoring the potential of microbiota-targeted therapeutic approaches (67). Conversely, dysbiosis-induced activation of the NLRP3 inflammasome, a central component of the innate immune system, links intestinal imbalance to systemic and neuroinflammatory cascades that contribute to cognitive impairment and neurodegenerative diseases, including Alzheimer's disease (68). Importantly, Mendelian randomization analyses have provided evidence supporting a bidirectional causal relationship between MGBA dysfunction and sleep disorders, reinforcing that microbial function and host pathophysiology are profoundly context dependent. This reciprocal interplay constitutes a fundamental mechanism underlying both the persistence and therapeutic refractoriness of sleep disturbances (66).

In recent years, the integration of multi-omics technologies, such as metagenomics, metabolomics, and transcriptomics, has significantly deepened our understanding of the MGBA and its role in sleep regulation. These approaches have identified specific microbial taxa such as Lactobacillus, Bifidobacterium, and Akkermansia muciniphila that influence tryptophan metabolism and melatonin synthesis, thereby providing a mechanistic explanation for their sleep-promoting effects. Moreover, metabolomic profiling in sleep-deprived models has revealed significant reductions in SCFAs, indole derivatives, and secondary bile acids—key mediators of gut-brain signaling. These findings underscore the power of systems biology approaches in delineating microbial-neurochemical interactions underlying sleep–wake homeostasis.

Within this framework, microbial metabolites function not only as mediators of gut-brain communication but also as initiators of neuroimmune cascades. Specifically, TLR4/NF-κB, ATP/P2X7R, and NLRP3/caspase-1 signaling axes form a self-sustaining inflammatory loop that amplifies neural dysfunction. LPS from dysbiotic Gram-negative bacteria prime the TLR4/NF-κB pathway, extracellular ATP released during sleep disruption activates P2X7R, and subsequent NLRP3-driven IL-1β secretion amplifies neuroinflammation and suppresses GABAergic transmission—hallmarks of insomnia and hyperarousal (69–71). Activated microglia further perpetuate this process by downregulating GABA synthesis and inhibitory tone, creating a persistent neuroinflammatory state that reinforces sleep fragmentation (72). Thus, the TLR4-P2X7R-NLRP3 axis represents a central pathological cascade linking gut-derived signals to neural excitability. Targeting this cascade may provide a mechanistic basis for next-generation therapies aimed at restoring sleep homeostasis and mitigating related neuropsychiatric comorbidities (Figure 2).

Building upon these mechanisms, emerging therapeutic strategies targeting the MGBA for sleep disorders demonstrate promising potential. The core strategy employs comprehensive, multi-pronged interventions such as microbiota-targeted interventions, herbal and multi-component pharmacological modulation, neural and neurochemical circuit regulation, metabolic and immune-inflammatory pathway modulation and chronobiological and circadian rhythm regulation, to achieve precise manipulation of the gut ecosystem. Emerging evidence strongly supports the efficacy of such strategies. Parallel to these developments, the field is moving toward personalized and precision-based microbiota therapeutics. Interindividual variability in microbial composition and metabolite profiles profoundly shapes responses to probiotics and fecal microbiota transplantation (FMT). Machine learning and artificial intelligence algorithms are increasingly being utilized to identify predictive microbial signatures associated with sleep quality and therapeutic responsiveness. Integrating clinical metadata, metagenomic datasets, and behavioral phenotypes through AI modeling may soon enable individualized microbial interventions that optimize treatment efficacy while minimizing adverse outcomes. Moreover, interventions that strengthen intestinal barrier integrity may reduce LPS translocation and subsequent systemic inflammation, thereby attenuating HPA axis overactivation and cortisol-mediated sleep disruption. Beyond traditional probiotics and FMT, next-generation microbiota-based therapeutics are emerging as promising modalities. Engineered bacterial consortia capable of synthesizing neurotransmitters (GABA, 5-HT) or anti-inflammatory metabolites (butyrate) have been developed to precisely modulate host neurochemistry (73). Synthetic biology and CRISPR-based technologies now enable the design of "designer microbes" that secrete targeted molecules directly within the intestinal lumen. In addition, dietary interventions rich in prebiotic fibers, polyphenols, and omega-3 fatty acids demonstrate synergistic effects with probiotic supplementation, suggesting that nutritional modulation of the MGBA may serve as a safe, noninvasive adjunct to pharmacotherapy. It is noteworthy that the development of future MGBA-targeted therapies should incorporate personalized and precision-based approaches, reflecting the considerable interindividual variation in GM composition shaped by genetic, environmental, dietary, and other factors (74).

Although the present review provides a comprehensive overview of the role of the MGBA in sleep disorders, several important limitations and controversies remain in this field. First, the causal relationship between GM alterations and sleep disturbances remains to be clarified. Most available evidence is derived from cross-sectional studies, which can only reveal correlations but not causality. Mendelian randomization analyses offer an alternative approach for causal inference, yet their conclusions are often constrained by the strength of genetic instruments, population specificity, and assumptions of linearity, thereby limiting the generalizability of findings (75). Second, the lack of repetition and methodological standardization in microbiome-based interventions represents a major obstacle to clinical translation. Despite growing enthusiasm for probiotic and FMT therapies, significant heterogeneity in strain selection, dosage, formulation, and delivery routes contributes to inconsistent outcomes across trials (76, 77). Even closely related Lactobacillus or Bifidobacterium strains can produce distinct molecular metabolites and elicit divergent host responses, underscoring the importance of strain-level precision (77). Variations in probiotic viability, administration duration, and host colonization capacity further complicate reproducibility (78). Similarly, the absence of standardized FMT protocols—including donor screening, microbial processing, concentration, and administration methods—results in substantial variability in efficacy and safety, hindering cross-study comparability and large-scale meta-analyses (76). Third, host-specific factors profoundly influence therapeutic responses. Genetic background, baseline microbiome composition, diet, sleep–wake rhythm, medication use, and environmental exposures all modulate the efficacy of MGBA-targeted interventions (79). For instance, individuals with distinct microbial enterotypes or metabolic capacities may respond differently to the same probiotic strain or FMT donor, suggesting that host-microbe compatibility is a key determinant of therapeutic success. Failure to account for these factors may explain much of the inconsistency observed across clinical trials (80). Fourth, current mechanistic studies heavily rely on animal models such as germ-free or sleep-deprived rodents. While these models are invaluable for hypothesis generation, substantial interspecies differences in physiology, sleep architecture, metabolism, and microbiome ecology limit the extrapolation of preclinical findings to humans (81). Moreover, many studies focus on single microbial metabolites or inflammatory biomarkers (IL-6, TNF-α, cortisol), without capturing the dynamic interplay among neurotransmitters (5-HT, dopamine, GABA), immune mediators, and endocrine pathways that jointly influence sleep regulation (82). Finally, clinical translation remains limited by methodological constraints, including small sample sizes, short follow-up periods, and inconsistent outcome evaluations, which collectively impede the reliable assessment of long-term efficacy and safety (83).

To overcome these challenges and unlock the therapeutic potential of the MGBA in sleep medicine, future research should focus on: (1) identifying functionally defined microbial strains and clarifying their mechanistic pathways; (2) developing standardized, reproducible protocols for probiotic and FMT interventions, with transparent reporting of strain taxonomy, viable CFU counts, formulation, donor screening, and administration routes; (3) integrating multi-omics and host phenotyping to capture host–microbe interactions and guide precision-microbiome therapeutics; (4) adopting large-scale, prospective, and mechanistically informed trials to establish causal and temporal relationships between microbiota dynamics and sleep disorders (84). Additionally, future investigations should explore circadian rhythm-microbiome interactions and sex-specific differences. Gut microbial activity displays diurnal rhythms that are synchronized with host circadian gene expression, and disruption of this alignment caused by shift work, jet lag, or chronic insomnia can lead to systemic metabolic disturbances and neuroinflammatory responses. Integrating chronobiological approaches into MGBA research could therefore reveal timing-based intervention strategies, while elucidating sex-related differences may provide insight into the higher prevalence of insomnia among females.

Given the multifactorial nature of sleep pathophysiology and the complexity of the MGBA, multimodal and personalized therapeutic strategies that integrate engineered microbial strains with nanotechnology-based delivery systems represent promising directions for future research (85). For example, nanomaterials can be designed to release therapeutic agents in response to specific microenvironmental cues, enabling spatiotemporal precision in microbial modulation (86). Such approaches may enhance bioavailability, improve targeting accuracy, and ultimately yield superior clinical efficacy.