design: DNA was extracted from streaks of pure cultures growing on plate count agar with milk and salt (PCAMS) plates using a MoBio PowerSoil DNA Isolation kit. Illumina sequencing libraries for each genome were constructed using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) using the manufacturers protocol with DNA input concentrations of 5-15 ng/L, a 20 minute fragmentase incubation for DNA fragmentation, and 5 rounds of PCR enrichment. Equimolar concentrations of each library representing isolate genomes were pooled and sequenced in one run on an Illumina HiSeq 2500 at the Harvard FAS Center for Systems Biology Core Facility.