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

<p></p><h1>Data sources</h1><br>This dataset was constructed using two different bioprojects:<br>PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.<br>PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.<br>PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.<br>PRJNA944553. 30 samples from 30 animals.<br>PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.<br>PRJNA923753 from Ho et al. 2023. 1 sample.<br><h1>Metagenomic assembly</h1><br>De 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.<br><h1>MAGs recovery</h1><br>MAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness &lt; 70% or contamination &gt; 5% or N50 &lt; 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).<br><h1>Non-redundant gene catalog</h1><br>Genes 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.<br><h1>MSPs recovery</h1><br>Samples 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.<br><h1>MAGs and MSPs taxonomic annotation</h1><br>Dereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.<br><h1>Construction of the phylogenetic tree</h1><br>39 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).<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters) for PRJEB4391, PRJEB9357, PRJNA758898, PRJNA906124, PRJNA908260, PRJNA923753 and PRJNA944553 used in catalogue assembly.<p></p>