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Background   Brachyspira  spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity.  Brachyspira intermedia  can cause production losses in chickens and strain PWS/A T  now becomes the fourth genome to be completed in the genus  Brachyspira .    Results  15 classes of unique and shared genes were analyzed in  B. intermedia, B. murdochii, B. hyodysenteriae  and  B. pilosicoli . The largest number of unique genes was found in  B. intermedia  and  B. murdochii . This indicates the presence of larger pan-genomes. In general, hypothetical protein annotations are overrepresented among the unique genes. A 3.2 kb plasmid was found in  B. intermedia  strain PWS/A T . The plasmid was also present in the  B. murdochii  strain but not in nine other  Brachyspira  isolates. Within the  Brachyspira  genomes, genes had been translocated and also frequently switched between leading and lagging strands, a process that can be followed by different AT-skews in the third positions of synonymous codons. We also found evidence that bacteriophages were being remodeled and genes incorporated into them.    Conclusions  The accessory gene pool shapes species-specific traits. It is also influenced by reductive genome evolution and horizontal gene transfer. Gene-transfer events can cross both species and genus boundaries and bacteriophages appear to play an important role in this process. A mechanism for horizontal gene transfer appears to be gene translocations leading to remodeling of bacteriophages in combination with broad tropism.

Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer