Clostridium difficile 6503
Whole genome shotgun sequence of strain was obtained using GS 20 DNA Library Preparation Kit and  GS-20 Genome sequencer (454 Life Sciences, Branford, CT)  following the manufacturer's standard procedures[Margulies et al, Nature 2005, 437(7057):376-380]. Briefly, bacterial genomic  DNA was extracted by using the Masterpure™ Gram positive Genomic DNA purification Kit (Epicenter Biotechnologies, Madison, WI) and spectrophotometrically quantified. Then, genomic DNA was fragmented by nebulization, ligated to specific adaptors and bound to Sepharose beads to obtain the single strand library, which was diluted and amplified by emulsion PCR. After recovery and washing, DNA beads were loaded onto a PicoTiterPlate where the DNA fragments were sequenced by pyrosequencing.