Long-read metagenomics to retrieve high-quality metagenome-assembled genomes from canine feces

"Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces" (BMC Genomics) We used nanopore long-read metagenomics and frame-shift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were >90% complete with <5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the taxonomic classification of the raw unassembled reads, the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs, which are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific, whereas others are more broadly distributed among animal and human microbiomes. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Moreover, we showed that long reads are key to gain biological insights that are otherwise missed in short-read MAGs catalogs, as shown by the mobilome functions detected in the long-read HQ MAGs. "Novel canine high-quality metagenome-assembled genomes, prophages, and host-associated plasmids by long-read metagenomics together with Hi-C proximity ligation" We characterized a canine fecal sample of a healthy dog by combining a long-read metagenomics assembly (Nanopore) with Hi-C cross-linking data and correcting frameshift errors. We retrieved and characterized 27 HQ MAGs and seven MQ MAGs considering MIMAG criteria. All the long-read canine MAGs (CanMAGs) improved previous short-read MAGs from public datasets regarding contiguity of the assembly, presence and completeness of ribosomal operons, and presence of canonical tRNAs. This trend was also observed for most comparisons with representative genomes from a pure culture (short-read assemblies). Moreover, Hi-C proximity ligation data linked potential plasmids to their bacterial hosts. Finally, we identified 51 bacteriophages integrated into their bacterial host, providing novel host information for eight viral clusters that included Gut Phage Database (GPD) viral genomes. Even though three viral clusters were species-specific, most of them presented a broader host range. In conclusion, long-read metagenomics retrieved long contigs harboring complete assembled ribosomal operons, prophages, and other mobile genetic elements. Hi-C binned together the long contigs into HQ and MQ MAGs, some of them representing closely related species. Moreover, Hi-C also linked plasmids to their bacterial host. Long-read metagenomics and Hi-C proximity ligation are likely to become a comprehensive approach to HQ MAGs discovery and assignment of extra-chromosomal elements to their bacterial host.