A. Cusco

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

This study uses long-read metagenomics and Hi-C to assemble high-quality canine MAGs and identify prophages and plasmids.

Rapid and real-time identification of fungi up to the species level with long amplicon Nanopore sequencing from clinical samples.

This study uses long amplicon Nanopore sequencing to identify fungi at the species level in clinical samples and demonstrates its effectiveness in detecting fungal communities in dogs with otitis.

Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer

This study uses Nanopore sequencing to analyze colistin resistance genes and other antibiotic resistance genes in pigs, cows, and farmers, identifying genetic contexts and transmission risks.

Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage

The paper uses shallow long-read metagenomics with Nanopore sequencing on pooled canine fecal samples to improve taxonomic resolution and identify an uncultured CrAssphage.

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon

This study evaluates long-amplicon PCR-based approaches using Nanopore sequencing for microbiota profiling at genus and species levels, finding that the rrn operon provides higher resolution than full-length 16S rRNA.