Quantifying live microbial load in human saliva samples over time reveals stable composition and dynamic load
This repository includes all data used in the analyses of this manuscript and scripts to reproduce the figures (with the exception of figure 1 (schematic) and figure 2D which was created using Empress).
T1_SMDS_metadata_ms.txt; Deidentified metadata with participant information and flow cytometry counts from the daily dynamics study that followed individuals across an ordinary day (n=88).
T2_SMDS_final_QF_table_wTaxa.biom; Quality filtered biom table of 16S rRNA gene amplicon sequencing data with taxonomy metadata (as described in methods) from the daily dynamics experiment (n=88).
T3_SRS_metadata_ms.txt; Deidentified metadata with participant information and flow cytometry counts from the acute perturbation experiment (n=84).
T4_SRS_final_QF_table_wTaxa.biom; Quality filtered biom table of 16S rRNA gene amplicon sequencing data with taxonomy metadata (as described in methods) from the acute perturbation experiment (n=78).
T5_metaphlan2_species.tsv; SMDS MetaPhlAn2 relative abundance output at the species level.
T6_humann2_pathways.tsv; SMDS HUMAnN2 relative abundance output at the pathway level.