Bacterial diversity of earthworm bed for rearing Eisenia fetida prepared using processed cow dung

Metagenomic DNA was isolated from processed cow dung using PowerSoil DNA Isolation kit (MO BIO Laboratories, Inc). DNA amplification of the V3 region of the 16S rRNA gene was carried out using Ion 16S Metagenomics kit (Thermo). Purification of the PCR amplicons was done using Purelink Quick Gel Extraction kit (Invitrogen). Amplicon quantification was performed using Qubit 4 Fluorometer (Thermo Fisher Scientific). Library preparation was carried out using Ion Plus Fragment Library kit (Thermo Fisher Scientific), in which, end-repairing and purification of the pooled amplicons were done first. then adapter-ligation and nick-repairing and purification of the products was done. Determination of library concentration was done using Ion Universal Library Quantitation kit (Thermo). Template preparation was done using Ion-PGM Hi-Q OT2 kit. The library was sequenced in Ion Torrent platform (Ion S5 system) using Ion PGM Hi-Q sequencing kit.