Cross-cohort meta-analysis reveals conserved gut microbiome signatures of insomnia

Insomnia is a prevalent sleep disorder associated with broad metabolic, immune, and neuropsychiatric consequences, yet its association with the gut microbiome remains difficult to define across individuals. Here, we performed a cross-cohort meta-analysis of five publicly available human fecal 16S rRNA case-control datasets to identify conserved microbiome features associated with insomnia. All raw sequencing data were reprocessed using a unified analytical workflow, generating a harmonized cohort of 468 individuals while controlling for cohort-specific effects. Across cohorts, insomnia was associated with directionally consistent differences in gut microbiome structure, including a statistically significant increase in Shannon diversity (p = 0.003) and a significant group effect after covariate adjustment. Integrating four complementary statistical approaches, we identified a core set of eight gut taxa that were consistently associated with insomnia across analyses. Functional prediction and integrative filtering indicated that insomnia-related microbial changes extended beyond taxonomy, with coordinated shifts in metabolic potential encompassing pathways previously linked to host immune and neurobiological processes, thereby suggesting relevance to biological systems implicated in sleep regulation. Notably, these functional alterations were concentrated within a limited subset of taxa rather than broadly distributed across the community. Among them, the Burkholderia-Caballeronia-Paraburkholderia complex emerged as a dominant functional contributor. Independent correlation analyses validated key taxon-function relationships and reinforced a model of focused, pathway-specific microbiome remodeling. Together, these findings demonstrate that insomnia is associated with a reproducible gut microbiome signature characterized by targeted functional remodeling driven by specific microbial taxa. This study provides a cross-cohort framework for investigating microbiome-mediated metabolic and immune contexts relevant to sleep regulation.