Novel canine high-quality metagenome-assembled genomes, prophages and host-associated plasmids provided by long-read metagenomics together with Hi-C proximity ligation

• DOI: 10.1099/mgen.0.000802
• Publication Date: 2022-03-17T17:17:29Z
• Authors: Anna Cuscó; Daniel Pérez; Joaquim Viñes; Norma Fàbregas; Olga Francino
• Keywords: Prophage

The human gut microbiome has been extensively studied, yet the canine is still largely unknown. availability of high-quality genomes essential in fields veterinary medicine and nutrition to unravel biological role key microbial members environment. Our aim was evaluate nanopore long-read metagenomics Hi-C (high-throughput chromosome conformation capture) proximity ligation provide metagenome-assembled (HQ MAGs) By combining ligation, we retrieved 27 HQ MAGs 7 medium-quality a faecal sample healthy dog. Canine (CanMAGs) improved genome contiguity representatives from animal MAG catalogues – short-read public datasets for species they represented: were more contiguous with complete ribosomal operons at least 18 canonical tRNAs. Both canine-specific bacterial generalists inhabit dog’s gastrointestinal Most them belonged Firmicutes , followed by Bacteroidota Proteobacteria . We also assembled one Actinobacteriota Fusobacteriota MAG. CanMAGs harboured antimicrobial-resistance genes (ARGs) prophages linked plasmids. ARGs conferring resistance tetracycline most predominant within CanMAGs, lincosamide macrolide ones. At functional level, carbohydrate transport metabolism variable mobilome function abundant some MAGs. Specifically, assigned functions associated mobile genetic elements host. 50 bacteriophages, providing novel bacterial-host information eight viral clusters, data six potential plasmids their Long-read are likely become comprehensive approach discovery assignment extra-chromosomal This will studying nutrition.