Functional redundancy and dissimilarity of bacterial communities and global bacterial genomes from GTDB

This datasets contains files (mostly taxa-by-trait matrices) that were used for the analysis of the functional redundancy and dissimilarity of bacterial communities from freshwater (microcosms) and from bacterial genomes accessed from the Genome Taxonomy Database (GTDB). The codes used for the analysis is also shared.MAGs_KO_input_alpha.csv: taxa-by-trait matrix for alpha diversityMAGs_ab_input_alpha.csv: taxa x abundance matrix for alpha diversitypMAGs_KO_input_beta.csv:taxa-by-trait matrix for beta diversitypMAGs_ab_input_beta.csv: taxa x abundance matrix for beta diversityMAGs_KO_input_gamma.csv: taxa-by-trait matrix for regional pool diversity (122 MAGs)df_GTDB.txt: taxa-by-trait matrix of 28 714 genomes from the GDTB88_taxa_alizee_gtdb-C10_renamed.treefile: Phylogenetic tree to assess beta MNTDmodified_Rao.Rlist_fun_2025.rds : List of KOs in each functional category (R version)List_functions_2025.csv: List of KOs in each functional category (as a dataframe)Code_Part1.R: Code to explore alpha, beta and overall taxa pool functional diversityCode_Part2.R: Code to explore GTDB genomes functional diversity and comparison with the MAGs from the experimental communities.