An updated catalog of genes and species of the pig gut microbiota

[Lien vers la fiche source] # Dataset overview We built an updated catalog of 9.3M genes found in the pig gut microbiota. Co-abundant genes were binned in 1523 Metagenomic Species Pan-genomes (MSPs) for which we provide taxonomic labels and a phylogenetic tree. In addition, we reconstituted 7059 Metagenome-Assembled Genomes (MAGs) covering of 760 Metagenomic Species and we extracted 7331 viral genomes from assemblies. Finally, we used Pairwise Comparative Modelling to predict 6140 antibiotic resistance genes. This dataset can be used to analyze shotgun sequencing data of the pig gut microbiota. # Methods ## Sequencing data availability Sequencing data from [Xiao et al.] (PRJEB11755, n=287) and [Kim et al.] (PRJEB32496, n=36) was downloaded from the European Nucleotide Archive. ## Sequencing data quality control Illumina adapters removal and read trimming was performed with [fastp ]. Reads mapped on the host genome (GCF_000003025.6) with [bowtie2] were removed with [samtools]. ## Metagenomic assembly Metagenomic assembly was performed with [metaSPAdes]. Contigs of less than 1500 bp were removed. ## MAGs creation Reads of each sample were aligned to their respective assembly with [bowtie2] and results were indexed in sorted bam files with [samtools]. Then, contigs coverage was computed in each sample with jgi_summarize_bam_contig_depths. MAGs were generated with [MetaBAT 2] and [MaxBin2]. Finally, results of both tools were combined with [DAS Tool] and MAGs quality was assessed with [checkM]. MAGs with completeness < 70% or contamination > 5% were discarded. ## Extraction of viral genomes Candidates viral sequences were identified in assemblies with [VirFinder]. Then, viral genomes quality was assessed with [checkV] and those low or undetermined quality were discarded. ## Non-redundant gene catalog Genes 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 ). The two non-redundant gene sets were merged by considering at first complete genes from the longest contigs (contact us for futher details). ## MSPs creation Using the Meteor software suite, reads from each sample were mapped against the non redundant catalog to build a raw gene abundance table (9.3 million genes quantified in 323 samples). This table was submitted to [MSPminer] that reconstituted 1523 clusters of co-abundant genes named Metagenomic-Species Pangenomes (MSPs). Quality control of each MSP was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles. ## Taxonomic annotation MAGs and MSPs were annotated with [GTDB-Tk] based on GTDB Release 05-RS95. ## Construction of the phylogenetic tree 39 universal phylogenetic markers genes were extracted from the 1523 MSPs (or the corresponding MAGs if available) 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). ## Prediction of antibiotic resistance genes Antibiotic resistance genes were predicted with the [Pairwise Comparative Modelling] approach (last version available [here]).