Long-read metagenomics to retrieve high-quality metagenome-assembled genomes from canine feces
About Anna Cuscó
Anna Cuscó is a researcher and project leader in Vetgenomics, a veterinary genetic diagnostics company focused on genomics and One-Health. Anna received her Ph.D. at the Universitat Autònoma de Barcelona and is now responsible for the microbiome and nanopore sequencing projects. Her research is focused on the canine microbiome and the application of novel technologies to characterize it.
We applied a nanopore-only metagenomics approach and retrieved eight single-contig high-quality metagenome-assembled genomes (HQ MAGs) and three medium-quality MAGs from a canine fecal sample. Among the HQ-MAGs, Succinivibrio represented a novel candidate bacterial species, whereas Sutterella represented the genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Four other HQ MAGs improved previous genome assemblies regarding contiguity and the number of rRNA and tRNA genes. Finally, both a high-molecular weight DNA extraction to improve contiguity, and correction of the insertions and deletions to reduce the frameshift errors, ensured the retrieval of complete single-contig HQ MAGs with nanopore-only reads.