DOI https://dx.doi.org/10.1038/s42255-021-00348-0

correspondence should be addressed to: [email protected],[email protected], or [email protected]

The content is divided into seperate Python and R scripts corresponding to different parts of the analysis presented in the paper:

Arivale cohort: 01_Arivale_analysis.md - microbiome processing, calculating alpha- and beta-diversity metrics for the Arivale cohort

02_Arivale_demographics_figure_2 - analysis reported in Figure 2

03_Metabolomics_figure_3.md - analysis reported in Figure 3

MrOS cohort:

MrOS_01_gut_microbiome.md - microbiome processing, calculating alpha- and beta-diversity metrics for the MrOS cohort

MrOS_02_Healthy_aging_analysis-spearman.md - analysis reported in Figure 4

MrOS_03_survival_analysis.md - analysis reported in Figure 5 and table 2

MrOS_04_differential_abundance_analysis.md - analysis reported in Figure 5