A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota. Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al. Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database) Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles. Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation. Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB22973 and PRJEB57230 (cohort used in catalogue assembly) and PRNJNA609596 (independent cohort not used in assembly).数据集概览 我们构建了一个包含褐家鼠（brown rat）肠道微生物组中590万个基因的目录。将共丰度基因聚类为1627个宏基因组物种（Metagenomic Species，MGS），并为其提供分类学标签。本数据集可用于分析褐家鼠肠道微生物组的鸟枪测序（shotgun sequencing）数据。 数据来源 本数据集来源于Mamiprooffi项目中通过鸟枪宏基因组测序（shotgun metagenomic sequencing）获得的大鼠粪便（及乳汁）样本。测序数据将尽快提交至欧洲核苷酸档案库（European Nucleotide Archive，ENA）的Bioproject PRJEB57230，同时纳入Pan等人发表的斯普拉格-道利大鼠（Sprague-Dawley rat）肠道宏基因组基因目录。 宏基因组组装 针对Mamiprooffi项目样本（数据源1），使用SPAdes组装软件进行宏基因组组装，参数设置为--iontorrent --careful。移除长度小于1500 bp的重叠群（contigs），以及与大鼠参考基因组Rnor_6.0成功比对的序列。 非冗余基因集 使用Prodigal基因预测软件对所有保留的重叠群进行基因预测，参数为-m -p meta。丢弃缺少起始密码子或长度小于99 bp的基因。随后，将完整基因与部分基因分别使用cd-hit-est进行聚类，参数为-c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0。最后，使用cd-hit-est-2d工具将上述两个非冗余基因集与已发表的基因目录（数据源2）进行合并，优先合并完整基因（如需进一步细节可联系我们）。 功能注释 使用KofamScan（版本1.3.0，匹配KEGG 107数据库）为最终基因目录中的基因注释KEGG同源基因簇（KEGG Orthologs，KOs）。 宏基因组物种 使用Meteor软件套件，将Bioproject PRJEB57230与PRJEB22973的样本测序reads比对至最终非冗余基因集，构建原始基因丰度表（共370个样本中定量了590万个基因）。将该丰度表提交至MSPminer与Canopy工具进行聚类，最终得到1627个共丰度基因簇，即宏基因组物种（MGS）。通过可视化标准化基因丰度谱热图，手动完成每个MGS的质量控制。 宏基因组物种的分类学注释 将所有核心基因与附属基因与基因组分类数据库（Genome Taxonomy Database，GTDB）r214代表基因组进行BLASTn比对，参数为版本2.10.1、task=megablast、word_size=16，保留每个基因的前20个最佳比对结果。若超过50%的基因匹配到同一GTDB代表基因组，且平均相似度≥95%、平均基因长度覆盖度≥90%，则为该MGS赋予物种水平注释。对于剩余的MGS，若超过50%的基因具有相同的分类学注释，则将其注释至更高分类层级（属至超界）。 公共队列的比对率分布 使用Meteor2工具（默认参数）生成比对率分布图谱，对比以下三个队列的比对性能：用于构建基因目录的PRJEB57230与PRJEB22973队列，以及未用于基因目录构建的独立队列PRJNA609596。