Enterosignatures define common bacterial guilds in the human gut microbiome (data)

Additional data related to the manuscript Enterosignatures define common bacterial guilds in the human gut microbiome.

The deposit contains the following files:

GMR_dataset.zip - data and results related to enterosignature computation in the GMR dataset: raw data, enterosignature composition, metabolic potentials of the associated metagenomic species

GMR_dataset
├── NMF_results # results of NMF decomposition, from k = 2 signatures to 10, 5 being the optimal number
│   ├── 10_H.tsv
│   ├── ....
│   ├── 9_W.tsv
│   └── README.txt
├── age_metadata.tsv # age of individuals in the GMR dataset
├── drama_MGS_gtdbtk_taxonomy.tsv # taxonomy of the MGS
├── drama_genus_level_abundance.tsv # genus-level abundance table used for NMF
└── metabo_data # Metabolic potential of the MGS associated to the enterosignatures
    ├── cazymes_by_genome.tsv # cazymes
    ├── gene_numbers.tsv # number of genes
    ├── kegg_metabolic_processes_by_genome.tsv # Kegg annotations
    ├── level1_onto_metabolites.tsv # Metacyc classes of metabolites, highest level
    ├── level2_onto_metabolites.tsv # Metacyc classes of metabolites, second level
    ├── metabolic_producers_full_community.tsv # predicted producers of metabolites, all genomes considered
    ├── metabolic_producers_withinES.tsv # predicted producers of metabolites, within an ES
    └── westerndiet.sbml # nutrients considered for metabolic modelling

BMIS_dataset.zip - data and results related to enterosignature computation in the BMIS dataset

BMIS_dataset
├── bmis_es_composition.tsv # ES assignments of BMIS samples (ES computed on the GMR dataset)
├── bmis_es_et_assignments.tsv # ES and enterotype assignments of BMIS samples
└── bmis_genus-level_abundance.tsv  # genus-level abundance matrix used for ES abundance computation

NonWestern_dataset.zip - data and results related to enterosignature computation in the non-western dataset

NonWestern_dataset
├── nonwestern_es_composition.tsv # ES assignments of Non-western samples (ES computed on the GMR dataset)
└── nonwestern_genus_abundance_normalised.tsv # genus-level abundance matrix used for ES abundance computation

The data is also available in the following repository: https://gitlab.inria.fr/cfrioux/enterosignature-paper/.

See also https://enterosignatures.quadram.ac.uk/.

本数据集关联论文《肠型特征（Enterosignatures）定义人类肠道微生物组中的常见细菌功能类群》。本数据集存档包含以下文件：

GMR_dataset.zip —— 关联GMR数据集肠型特征计算的相关数据与结果，包含原始数据、肠型特征组成、关联宏基因组物种（metagenomic species, MGS）的代谢潜能数据。
GMR_dataset
├── NMF_results # 非负矩阵分解（NMF）分解结果，涵盖特征数k=2至k=10的结果，最优特征数为5
│   ├── 10_H.tsv
│   ├── ....
│   ├── 9_W.tsv
│   └── README.txt
├── age_metadata.tsv # GMR数据集个体的年龄元数据
├── drama_MGS_gtdbtk_taxonomy.tsv # 宏基因组物种的分类学注释信息
├── drama_genus_level_abundance.tsv # 用于NMF分析的属级丰度表
└── metabo_data # 与肠型特征关联的宏基因组物种的代谢潜能数据
    ├── cazymes_by_genome.tsv # 碳水化合物活性酶（CAZymes）注释文件
    ├── gene_numbers.tsv # 基因数量统计文件
    ├── kegg_metabolic_processes_by_genome.tsv # 京都基因与基因组百科全书（KEGG）代谢过程注释文件
    ├── level1_onto_metabolites.tsv # 代谢物的MetaCyc一级分类层级
    ├── level2_onto_metabolites.tsv # 代谢物的MetaCyc二级分类层级
    ├── metabolic_producers_full_community.tsv # 全基因组范围预测的代谢物产生菌
    ├── metabolic_producers_withinES.tsv # 肠型特征范围内预测的代谢物产生菌
    └── westerndiet.sbml # 代谢建模所用的系统生物学标记语言（SBML）格式营养物质配置文件

BMIS_dataset.zip —— 关联BMIS数据集肠型特征计算的相关数据与结果。
BMIS_dataset
├── bmis_es_composition.tsv # BMIS样本的肠型特征归属（肠型特征基于GMR数据集计算得到）
├── bmis_es_et_assignments.tsv # BMIS样本的肠型特征与肠型归属信息
└── bmis_genus-level_abundance.tsv # 用于肠型特征丰度计算的属级丰度矩阵

NonWestern_dataset.zip —— 关联非西方人群数据集肠型特征计算的相关数据与结果。
NonWestern_dataset
├── nonwestern_es_composition.tsv # 非西方人群样本的肠型特征归属（肠型特征基于GMR数据集计算得到）
└── nonwestern_genus_abundance_normalised.tsv # 用于肠型特征丰度计算的标准化属级丰度矩阵

本数据集亦可通过以下存储库获取：https://gitlab.inria.fr/cfrioux/enterosignature-paper/。
另可参考：https://enterosignatures.quadram.ac.uk/。