Gut Isolates from a Antidepressant-Treated Patients and its Potential Antibiotic Resistance Induction Genome sequencing and assembly
To perform gDNA isolation, the protocol of PureLink Genomic DNA Kit (Thermo Fisher Scientific, 2024) was followed with minor adjustments to increase cell lysis. Plasmid isolation was done with a traditional method for plasmid isolation involves alkaline lysis followed by ethanol precipitation. Whole genome short read sequencing of all three strains was performed on iSeq100 platform with a 300-cycle iSeq reagent kit generating paired-end (2x150bp) raw reads. Here, libraries were prepared using standard protocols for Illumina DNA Prep Kit and NexteraTM CD indexes. De novo assembly of short-reads were performed with SPAdes (v.3.15.5). The genome assembly was checked using QUAST (v.5.3.0) and annotation was performed with Prokka (v.1.14.6).