Sleep Deprivation Alters Gut Microbiome Diversity and Taxonomy: A Systematic Review and Meta-Analysis of Human and Rodent Studies

Sleep deprivation (SD) affects the gut microbiome, but findings across studies vary in terms of microbiota changes, SD induction methods and gut measurements. The effects of SD on the gut microbiome in humans and rodents have not been comprehensively reviewed. This meta-analysis investigated SD-related factors and their effects on the gut microbiome in human and rodent models. We analysed data from studies published before February 28, 2024, and calculated standardised mean differences (SMDs). Subgroup analyses were conducted for rodents and humans. A total of 20 studies (4 human, 5 rat, 8 mouse and 3 combined human and rodent) were included. SD significantly reduced alpha diversity (Shannon and Simpson indices) and increased the Firmicutes-to-Bacteroidetes ratio. In rodents, the Shannon index was lower (SMD = −1.27, 95% CI: −2.20 to −0.34), and the Firmicutes/Bacteroidetes ratio was higher (SMD = 2.60, 95% CI: 1.61–3.59). Human studies showed nonsignificant trends, limited by small sample sizes. Analysis at the phylum, family and genus levels showed a modest decrease in Actinobacteria and Tenericutes and a minor increase in Bacteroidetes, Firmicutes and Proteobacteria. Reductions in Lactobacillaceae and Erysipelotrichaceae and increases in Ruminococcaceae and Lachnospiraceae were observed. A2, Lactobacillus and Ruminococcus_1 were less abundant in the SD group. Overall, SD alters gut microbiome composition. Standardised human studies are needed to clarify translational relevance.