Novel canine high-quality metagenome-assembled genomes, prophages and host-associated plasmids provided by long-read metagenomics together with Hi-C proximity ligation
Cuscó, Anna (Universitat Autònoma de Barcelona. Vetgenomics)
Pérez, Daniel (Universitat Autònoma de Barcelona. Servei Veterinari de Genètica Molecular (SVGM))
Viñes, Joaquim (Universitat Autònoma de Barcelona. Servei Veterinari de Genètica Molecular (SVGM))
Fábregas, Norma (Universitat Autònoma de Barcelona. Vetgenomics)
Francino, Olga (Universitat Autònoma de Barcelona. Servei Veterinari de Genètica Molecular (SVGM))

Date:	2022
Abstract:	The human gut microbiome has been extensively studied, yet the canine gut microbiome is still largely unknown. The availability of high-quality genomes is essential in the fields of veterinary medicine and nutrition to unravel the biological role of key microbial members in the canine gut environment. Our aim was to evaluate nanopore long-read metagenomics and Hi-C (high-throughput chromosome conformation capture) proximity ligation to provide high-quality metagenome-assembled genomes (HQ MAGs) of the canine gut environment. By combining nanopore long-read metagenomics and Hi-C proximity ligation, we retrieved 27 HQ MAGs and 7 medium-quality MAGs of a faecal sample of a healthy dog. Canine MAGs (CanMAGs) improved genome contiguity of representatives from the animal and human MAG catalogues - short-read MAGs from public datasets - for the species they represented: they were more contiguous with complete ribosomal operons and at least 18 canonical tRNAs. Both canine-specific bacterial species and gut generalists inhabit the dog's gastrointestinal environment. Most of them belonged to , followed by and . We also assembled one and one MAG. CanMAGs harboured antimicrobial-resistance genes (ARGs) and prophages and were linked to plasmids. ARGs conferring resistance to tetracycline were most predominant within CanMAGs, followed by lincosamide and macrolide ones. At the functional level, carbohydrate transport and metabolism was the most variable within the CanMAGs, and mobilome function was abundant in some MAGs. Specifically, we assigned the mobilome functions and the associated mobile genetic elements to the bacterial host. The CanMAGs harboured 50 bacteriophages, providing novel bacterial-host information for eight viral clusters, and Hi-C proximity ligation data linked the six potential plasmids to their bacterial host. Long-read metagenomics and Hi-C proximity ligation are likely to become a comprehensive approach to HQ MAG discovery and assignment of extra-chromosomal elements to their bacterial host. This will provide essential information for studying the canine gut microbiome in veterinary medicine and animal nutrition.
Grants:	Ministerio de Ciencia, Innovación y Universidades PTQ2018-009961
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Canine metagenome ; Gut microbiome ; Hi-C proximity ligation ; Long-read metagenomics ; Metagenome-assembled genomes ; Nanopore
Published in:	Microbial Genomics, Vol. 8 (march 2022) , ISSN 2057-5858

DOI: 10.1099/mgen.0.000802
PMID: 35298370

15 p, 2.2 MB

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