Long-read metagenomics of Shanghai pet dogs

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort by Anna Cuscó, Yiqian Duan, Fernando Gil, Alexei Chklovski, Nithya Kruthi, Shaojun Pan, Sofia Forslund, Susanne Lau, Ulrike Löber, Xing-Ming Zhao, and Luis Pedro Coelho (bioRxiv PREPRINT 2025) We used deep long-read sequencing (ONT), polished with short reads (Illumina), on stool samples from 51 pet dogs in Shanghai. Raw data (Nanopore, and Illumina), and MAG catalog (fasta files) are available on ENA under Bioproject ID PRJEB85799.In this repository, we make available MAG annotations and other derived datasets to be further explored and used: Metagenome-assembled genomes (MAG) catalog annotations: Shanghai Dog MAG catalog contains 2,676 MAGs that belong to 320 different bacterial species. Here, we provide: Extracted rRNA genes (SHD1_rRNAs_fasta_barrnap.tar.gz), MAGs annotations using eggnog-mapper (SHD1_eggNOG_MAG_annotations.tar.gz) MAGs annotations using RGI (SHD1_ARGs_MAGs.csv.gz), and contig-level annotations using RGI (SHD1_ARGs_contigs.csv.gz) Extrachromosomal elements (ECEs) catalog (SHD1_EC.fna.gz): includes 185 single-contig circular elements (non-redundant). We identified 58 plasmids, 30 viruses, and 97 uncategorized elements (SHD1_EC_props.tsv.gz) Gene catalog: includes 1,470,802 non-redundant genes (95% nucleotide identity, representing species-level unigenes). Of these, 98.7% are complete genes, and 73.5% are contained in MAGs or ECEs. Conceptually, there are three levels: (1) ORFs, the original open read frames (in the file SHD1_GC.ORF.fna.xz with associated metadata in SHD1_GC.ORF.orig.tsv.xz), (2) clustered ORFs at 100% nucleotide identity (in SHD1_GC.100NT.fna.xz), and (3) clustered ORFs at 95% nucleotide identity (in SHD1_GC.95NT.fna.xz and SHD1_GC.95NT.faa.xz, for nucleotide and amino acid sequences, respectively). The 100% clustered ORFs are a subset of the original ORFs, and the 95% clustered ORFs are a subset of the 100% clustered ORFs (these relationships are in the file SHD1_GC.clusters.tsv.xz. Eggnog-mapper annotations (in SHD1_GC.95NT.emapper.annotations.gz) are provided for the 95% clustered ORFs. Small ORFs catalog: includes 403,491 non-redundant smORFs, which produce 273,065 clusters at 90% identity. The extracted smORFs, clustered at 100% amino acid identity are available in provided (SHD1_SM.100AA.faa.gz with associated metadata in SHD1_SM.100AA_origins.tsv.gz, note that same sequence identifier may be listed multiple times as identical sequences may be present in multiple samples). We also provide 90% amino acid clusterings (FASTA in SHD1_SM.90AA.faa.gz, with clustering in SHD1_SM.clusters.tsv.gz).).