From alpha diversity to zeitgebers: Bacterial gut microbiome associations with sleep and circadian disruption (Part I)

Sleep is a vital behavioral state influencing multiple body systems, including the gut-brain axis, which involves bidirectional communication between the brain and gastrointestinal system. This scoping review examines and provides a comprehensive overview of literature examining the relationship between sleep and the gut microbiome to identify literature gaps. Seventy-four preclinical rodent studies and 65 human translational studies reporting direct sleep and gut microbiome associations were synthesized. We found variable alpha diversity responses to sleep pathology, with decreased alpha diversity more consistent in longer sleep disruption periods. Preclinical studies showed variable phylum-level responses, while in humans, sleep disruption was linked to decreased Bacillota and circadian disruption to increased Bacillota. Unhealthy sleep patterns were commonly associated with reduced levels of beneficial genera such as Faecalibacterium and Lactobacillus, and increased Clostridium, though findings were not consistent across all studies. Recommendations are made to ensure rigorous, reproducible research in this field. The potential for gut microbiome modulation as a therapeutic target is highlighted, with suggested future research directions for preventing sleep disruption and pathology.