Metagenomics of "Bradypus crinitus": Feces
Virome metagenomics by shotgun and size selection: The samples were vortexed until complete homogenization. Then, approximately 1 mL of sample was transferred to the extraction bead tube (MP Biomedicals, CA, USA) to break up the debris. The supernatant was collected from each sample and an equimolar volume was pooled in one single tube. The next step was Illumina library construction, following the general CDC protocol methodology (Kohl et al., 2015) with previously described modifications (Cosentino et al., 2022). HTS was conducted on an Illumina MiSeq platform using the MiSeq V2 cartridge with pair-ended 2x151 cycles. Sequencing data was processed with a custom pipeline (Cosentino et al., 2022). To avoid false positive results due to sequencing index-hoping (Farouni et al., 2020), we considered as invalid the identification of a viral family when it was detected by a number of reads that was less than 1% of the highest count identified for the same family among all other libraries sequenced in the same run.