Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study

Processed data as Supplementary Dataset to support Nature Communications publication. metadata.xlsx contains the following worksheets: R - metadata for study taxa - Taxonomic assignment abundance table pwy - Metacyc pathway abundance table with Metacyc identity codes pwynames - Metacyc pathway names and identity codes. ec - functional genes EC identity codes. ecnames - EC names and identity codes cardnames - Antibiotic resistance genes and CARD identity codes card - CARD abundance table with antibiotic resistance identity codes 2. mpa_vOct22_CHOCOPhlAnSGB_202212_SGB2GTDB.tsv contains the single genome bin (SGB) identity codes and taxonomic assignment. Species assigned as single genome bins were manually assigned the taxonomic identity based on Chocophlan database 2022. The following are statistical results for the corresponding figures 3. FIG_4B_and Supplementary_Fig_5_ST131_carriage_dunn.csv: Dunn's test for taxa in Fig. 4b and Supplementary Fig. 5. 4. FIG_4D_pwy_bubble_plot_pvalues.csv: Statistical results of metacyc pathway. 5. FIG_5_ec_ecoli_spearman_correlation.csv: Spearman correlation iucABCD genes results. 6 to 9 Statistical results relating to Figure 7: Two-way wilcoxon rank sum tests between persistent vs non-carriers; persistent vs intermittent for taxonomic and metabolic features identified using Random forest. 10. Supplemenary_Fig1_adonis2_results.csv: PERMANOVA multivariate statistical result. 11. Supplementary_Fig_2_taxa_hd_exposure_boxplots_pvalues.csv: Statistical results for household transmission risk. 12. Supplementary_Fig_3_statistical_results_boxplots.csv: Kruskal-Wallis and Dunn's test for antibiotic naive samples. 13. Supplementary_Fig_4_st131_detection_Wilcoxon.csv: Wilcoxon test results between ST131 detection groups. 14. Supplementary_Fig_5_ST131_carriage_dunn.csv: Dunn's test result between host carriage status. 15. Supplementary_Fig_5_ST131_carriage_kruskal.csv: Dunn's test result between host carriage status. 16. Storms checklist. 17. The GITHUB repository https://github.com/gmml-nus/ST131-persistence-microbiome contains: R codes to Figures 1 to 7 LR_results- Linear regression statistical results folder in csv and R codes