... you know, the Bacillus subtilis contaminant that was found alongside the Bacillus anthracis isolate which was used by the Anthrax Killer?
As other people have noted, B. anthracis is a very clonal organism. What this means is that individual strains are highly similar to each other, there is not a whole lot of diversity. On the other hand, B. subtilis has a high degree of heterogeneity within its genome. What does this mean? It means that B. subtilis is much easier to type (or differentiate) from other strains of B. subtilis.
Yeah, but B. subtilis was a contaminant. What's the big deal? Well, the devil is often in the details. Bruce Ivins worked on B. subtilis. In 2003, Ivins published a paper looking at expression of B. anthracis genes in B. subtilis, and how that effected immune responses in guinea pigs. The link to the paper is above, free of charge as all government publications are considered public domain.
Ok, so what? Well ... since B. subtilis (Bs) has a higher degree of heterogeneity within its genome, it is easier to type. For example: Bs in Lab B, if it didn't receive the strain from Lab A, will most likely hold more differences than Bs in Lab A ... when compared to B. anthracis (Ba) isolates from those two labs. What this means is ... if you have isolates of Ba AND Bs in Lab A, and another set of isolates of Ba and Bs in Lab B, it's easier to type the Bs isolates.
Make sense? So essentially, the FBI probably wasn't as concerned with the Ba in the letters as we might suspect. A goodly portion of the investigation could very well have been focused on the Bs contaminant found in some of the letters. Then, taking multiple Bs isolates from around the world, they probably typed those strains (which would be much easier to do than typing Ba isolates as the Bs isolates have more differences in their genome) to see if Ivins' Bs strain matched the one in the envelopes. I'm not sure if the results have been posted, but I imagine it did. Of course, this probably raises a lot of issues ... like whether or not he gave that Bs strain to anyone ... but it might shed a little more detail on the scientific aspects of this case.