Optical restriction mapping [31, 32, 33] was used to compare the overall genomic structure of selected isolates. No differencesin overall genome architecture between the ''military'' BG isolates, the archival 1942 isolate, or 1013-1 were observed (Figure 4 , data not shown), suggesting that the global architecture of these isolates is relatively stable, even over 30 years of serial in vitro passage.However, the optical maps and sequence coverage analysis of 1013-2 and 9372-1revealed substantial deletions of approximately 72,727and 23,678 bases, respectively, of genomic materialspanning from positions 3,992,613 to 4,065,341 (1013-2) or 4,022,138-4,045,817 (ATCC 9372-1) (Figure 4 ; Table S2 ). The genes within this deleted region are listed in Table S3 but notably contain genes encoding for nitrite reduction, germination (gerKABC), and biosynthesis of the lipopeptide surfactin (srfCAB) [34, 35] . A defect in surfactin production is a particularly intriguing candidate for the morphology and pigmentation variations in 1013-2 and ATCC 9372-1, since disruption of srfA has been shown to have dramatic effects on spreading motility on semisolid media, on biofilm formation [34, 36] , and low-grade hemolytic activity.