To gain insight into the effects of genetic divergence of the adapted isolates on their metabolic capacity, the Detrick isolates and the separate 1013 isolates were compared by multiphenotype analysis using the Omnilog system, which allows the highthroughput comparison of 96620 discrete growth conditions, including carbon, nitrogen, phosphorus, sulfate, nutrient supplements, pH, osmolytes as well as a broad class of growth inhibitors. The growth of the 1942 strain was used as a reference for determining relative growth rates of the other strains. The results of Mutations exhibiting high quality scores in both reference and query sequences and with differences from the template exhibited in .85% of the individual sequencing reads are indicated as a blackened box. In one case (position 259001 in ATCC 9372-1) an initial false-negative due to the formation of a homopolymeric tract was found by direct inspection of the assemblies. The genes whose functions are altered by the given mutation are indicated in Table 4 these experiments are summarized in Figure 6 and Table S4 . In general, growth of the 1013 isolates was significantly diminished relative to the 1942 in many different growth conditions, most notably in the ability to use amino acids and peptides as carbon and nitrogen sources, to withstand osmotic stress, and to grow under reduced pH. In addition, the strains had developed sensitivity to beta-lactams, quinolones, and membrane-disrupting activities. These results suggested broad combined effects of several mutations on the phenotype of the strains. In addition to the spo0F(A98P) allele, which is a likely candidate for highly pleiotropic effects on the decision to sporulate under many different conditions, both strains contain substitutions in the yetF and yqgE genes that may be contributing to the phenotypes observed. The more pronounced defect in 1013-2 may be attributable to defects in the gerAB and gerAC genes and the large 72 kb deletion which contains several genes involved in germination. By contrast, the Detrick isolates in general grew more robustly than the 1942 strain under multiple growth conditions. Increased relative growth rates were particularly pronounced for acidic conditions and media containing osmolytes, but particularly for wells containing sodium lactate [6] .