SRX2793829 Mlepmu3 SRP106761 PRJNA384500 DNA was extracted from isolated bacteria grown in Balb/c mice. Fifty ?l of DNA was sonicated with the S220 Covaris to obtain 400 bp-long DNA fragments and purified using AMPure beads (1.8X). After quantification with the Qubit dsDNA HS assay and the Qubit Fluorometer, up to 1 ?g of DNA in 50 ?l was used for library preparation using the Kapa Hyper prep kit (Roche) and the PentAdapters (Pentabase) for indexing. The library was quantified using the Qubit dsDNA BR assay and the Qubit Fluorometer. SRS2175020 SAMN06841017 Mlepmu3 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX2793830 m160830 SRP106761 PRJNA384500 DNA was extracted from isolated bacteria grown in Balb/c mice. The DNA was sheared in a Covaris g-TUBE (Covaris, Woburn, MA, USA) to obtain 10 kb fragments. After shearing the DNA size distribution was checked on a Fragment Analyzer (Advanced Analytical Technologies, Ames, IA, USA). 4 ľg of the sheared DNA was used to prepare a SMRTbell library with the PacBio SMRTbell Template Prep Kit 1 (Pacific Biosciences, Menlo Park, CA, USA) according to the manufacturer's recommendations. The resulting library was size selected on a BluePippin system (Sage Science, Inc. Beverly, MA, USA) for molecules larger than 8 kb. The recovered library was sequenced on one SMRT cell with P6/C4 chemistry and MagBeads on a PacBio RSII system at 240 min movie length. SRS2175020 SAMN06841017 m160830 WGS GENOMIC RANDOM PacBio RS II