A catalog of genes, genomes and species of the cat (Felis catus) intestinal microbiota

Data sourcesThis dataset was constructed using two different bioprojects:PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.PRJNA944553. 30 samples from 30 animals.PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.PRJNA923753 from Ho et al. 2023. 1 sample. Metagenomic assemblyDe novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed. MAGs recoveryMAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%). Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives. MSPs recoverySamples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer. MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs. Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni). Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters) for PRJEB4391, PRJEB9357, PRJNA758898, PRJNA906124, PRJNA908260, PRJNA923753 and PRJNA944553 used in catalogue assembly.数据来源：本数据集依托六项不同的生物项目构建： 1. 来自Ma等人2022年研究的PRJNA758898，包含16只动物的16份样本； 2. 来自Deusch等人2015年研究的PRJEB9357，包含30只动物的88份样本； 3. 来自Deusch等人2014年研究的PRJEB4391，包含18只动物的36份样本； 4. PRJNA944553，包含30只动物的30份样本； 5. 来自Bai等人2023年研究的PRJNA908260，包含8只动物的8份样本； 6. 来自Ho等人2023年研究的PRJNA923753，包含1份样本。 宏基因组组装：对上述所有样本执行宏基因组从头组装。首先使用fastp去除测序接头并修剪测序读段；随后利用bowtie2将比对至宿主基因组（GCF_018350175.1）的读段通过samtools过滤移除；最终使用metaSPAdes完成宏基因组组装，并剔除长度小于1500 bp的重叠群（contig）。 宏基因组组装基因组（Metagenome-Assembled Genomes, MAGs）恢复：使用COMEBin（多重覆盖度模式）生成MAGs，并通过CheckM2评估其质量。剔除完整度低于70%、污染率高于5%或N50小于5 Kb的MAGs。使用fastANI计算所有已恢复的MAGs的两两平均核苷酸一致性（Average Nucleotide Identity, ANI），并以95%的ANI阈值在物种水平进行去冗余操作。 非冗余基因集构建：使用Prodigal（参数：-m -p meta）对所有宏基因组组装得到的重叠群进行基因预测。将预测得到的基因合并后，通过cd-hit-est（参数：-c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0）进行聚类，并选取最长重叠群上的基因作为代表序列。 宏基因组物种泛基因组（Metagenomic Species Pan-genomes, MSPs）恢复：将多队列样本（上述所有项目加上来自Lee等人2022年研究的PRJNA906124）与非冗余基因集进行比对，使用Meteor软件套件生成原始基因丰度表（共在212份样本中定量了130万个基因）。随后利用MSPminer将共丰度基因聚类为344个MSPs，即归属同一微生物物种的基因簇集合。 MAGs与MSPs分类注释：使用基于GTDB r214的GTDB-Tk对去冗余后的MAGs进行分类注释，并将MAGs的分类信息传递至对应的MSPs。 系统发育树构建：使用fetchMGs从去冗余后的MAGs中提取39个通用系统发育标记基因，随后使用MUSCLE分别对各标记基因进行多序列比对。将40份比对结果合并后，使用trimAl（参数：-automated1）进行序列修剪。最终通过FastTreeMP（参数：-gamma -pseudo -spr -mlacc 3 -slownni）构建系统发育树。 公共队列比对率分布：针对本数据集构建时用到的PRJEB4391、PRJEB9357、PRJNA758898、PRJNA906124、PRJNA908260、PRJNA923753及PRJNA944553队列，使用Meteor2（默认参数）生成比对率分布图谱。