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.本数据集包含多种文件（多为物种-性状矩阵），用于分析淡水微宇宙环境细菌群落以及从基因组分类数据库（Genome Taxonomy Database, GTDB）获取的细菌基因组的功能冗余性与相异性。本次分析所用的代码亦随数据集一并共享。 - MAGs_KO_input_alpha.csv：用于α多样性分析的物种-性状矩阵 - MAGs_ab_input_alpha.csv：用于α多样性分析的物种-丰度矩阵 - pMAGs_KO_input_beta.csv：用于β多样性分析的物种-性状矩阵 - pMAGs_ab_input_beta.csv：用于β多样性分析的物种-丰度矩阵 - MAGs_KO_input_gamma.csv：用于区域群落库多样性分析的物种-性状矩阵（含122个宏基因组组装基因组（Metagenome-Assembled Genomes, MAGs）） - df_GTDB.txt：来自GTDB的28714个基因组的物种-性状矩阵 - 88_taxa_alizee_gtdb-C10_renamed.treefile：用于评估β多样性最近分类单元平均距离（beta MNTD）的系统发育树 - modified_Rao.R：分析脚本文件 - list_fun_2025.rds：各功能类别中KEGG正交基因（KOs）的列表（R语言格式） - List_functions_2025.csv：各功能类别中KOs的列表（数据框格式） - Code_Part1.R：用于探索α、β及整体物种库功能多样性的代码 - Code_Part2.R：用于探索GTDB基因组功能多样性并与实验群落宏基因组组装基因组进行对比的代码