Fecal Microbiota Features Associated with Short Sleep and Depression in Older Adults: A Cross-Sectional Analysis of the American Gut Project

Background: Short sleep and depression frequently co-occur in older adults, but whether they share a gut microbiota signature or carry largely phenotype-specific features remains unresolved. We therefore characterized fecal microbiota features shared by or specific to short sleep and depression using American Gut Project 16S rRNA data. Methods: Using American Gut Project (AGP) V4 16S rRNA data (PRJEB11419), we assigned older adults to four mutually exclusive groups: healthy controls (HC; 7-8 h sleep, no depression), short-sleep only (SSD), depression only (DP), and short-sleep plus depression (SSD + DP; exploratory). Complete age, sex, and BMI data with at least 1,000 reads yielded 1,056 participants (HC 617; SSD 255; DP 148; SSD + DP 36). We examined diversity, taxonomy, covariate-adjusted genus-level associations, and cross-validated discrimination. Scale-upgraded sensitivity analyses included 1,307 participants, 146 genera, and 20 multiply imputed data sets. Results: Richness (q = 0.001; adjusted q = 0.007), Shannon diversity (q = 0.031; adjusted q = 0.111), and Faith's diversity (q = 0.001; adjusted q = 0.007) differed across groups; adjusted richness and Faith's diversity also differed among depression-only participants (both q = 0.003). PERMANOVA showed no global separation (minimum P = 0.065). Significant genera numbered 3 in SSD, 3 in DP, and 0 in SSD + DP: SSD was associated with UCG-002 (log2FC = -1.01), UCG-003 (-0.76), and Erysipelatoclostridium (+0.69), and DP with UCG-003 (-1.21), [Ruminococcus] gnavus group (+1.06), and Lachnospiraceae UCG-010 (-0.71). Core clinical AUCs were 0.554 (95% CI 0.514-0.596) and 0.623 (0.579-0.668), rising to 0.599 (0.559-0.640) and 0.654 (0.611-0.695) with extended clinical variables; adding microbiota features lowered these to 0.566 (0.524-0.608) and 0.637 (0.593-0.680), providing no gain. Sensitivity AUCs were 0.575-0.610 and 0.643-0.675. Scale-upgraded OLS/limma confirmed 17 genera and 8 interaction genera, with AUCs of 0.585 and 0.645; additional models reached 0.622 and 0.687. A phenotype-matched constipation contrast (78 cases, 695 controls) yielded AUCs of 0.771 and 0.798. Conclusion: Short sleep and depression showed modest, largely non-overlapping microbiota signals, whereas constipation showed a clearer but still non-diagnostic signal. These findings are hypothesis-generating and do not support clinical or causal interpretation.