Bacteria
For library preparation, the Illumina Nextera DNA Flex Library Prep now called Illumina DNA Prep (Cat. No. 20025519, 20025520, 20018704, and 20018705) was used with 100 ng DNA (nucleic acid) received. The sequencing ready libraries were prepared as instructed by the manufacturer. The quality of the prepared library was checked by performing the agarose gel electrophoresis (2% Agarose gel), libraries were quantified using the qubit instrument and DNA HS kit (Invitrogen). Library concentrations were adjusted to 4 nM and pooled for multiplex sequencing. Pooled libraries were denatured and diluted at 300 pM and loaded in the library tube provided with the NovaSeq SP sequencing kits (300 cycles). The pooled libraries were further processed for paired end (2 X 151 bp) sequencing on Illumina NovaSeq6000 instrument.