In order to reproduce the results from the manuscript, follow the notebooks provided on OSF in the order listed below. Due to personal health information associated with this study, the full sample-information files are only available via a data useage agreement. See manuscript for details on obtaining these via the MrOS online portal. Of note, many of the QIIME 2 artifacts store sample metadata files within their provenance folder which means that unfortunately I cannot share those either. However, once the metadata file is obtained the below will guide on reproducing the study completely. 1. `metadata_cleaning_MrOS_March_2022.Rmd` or its html version. This just shows how the metadata file was curated. Not needed to run for reproduction. The outcome of this script is a metadata file called `q2_mros_sleep_metadata.tsv` which is needed for next step. 2. `CVD_and_sleepstudy_microbiome_merging_runs.ipnyb` <- this notebook describes how we go from Qiita-derived feature-table and phylogenetic tree to a filtered version specific to this study, which we then use in the next notebook. 3. `MrOS_sleepstudy_qiime2_processing_Mar_2022.ipnyb` <- this notebook shows how we take our processed table and tree and use it to run diversity analyses. 4. `alpha_diversity_mros_sleep_March_2022.Rmd` <- our alpha diversity analysis 5. `beta_diversity_mros_sleep_March_2022.Rmd` <- out beta diversity analysis, including db-RDA and PERANOVAs. As a heads up this notebook can take up to an hour to run! 6. `DA_mros_sleep_March_2022.Rmd` <- CoDaCoRe differential abundance analysis. 7. `logratio_plots_MrOS_sleep_microbiome_March_2022.Rmd` <- creates the log ratio plots in the manuscript If you run into any issues please don't hesitate to contact me at mestaki@gmail.com and I will be happy to help you navigate through the code.