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Background  The anaerobic spirochaete  Brachyspira pilosicoli  causes enteric disease in avian, porcine and human hosts, amongst others. To date, the only available genome sequence of  B. pilosicoli  is that of strain 95/1000, a porcine isolate. In the first intra-species genome comparison within the  Brachyspira  genus, we report the whole genome sequence of  B. pilosicoli  B2904, an avian isolate, the incomplete genome sequence of  B. pilosicoli  WesB, a human isolate, and the comparisons with  B. pilosicoli  95/1000. We also draw on incomplete genome sequences from three other  Brachyspira  species. Finally we report the first application of the high-throughput Biolog phenotype screening tool on the  B. pilosicoli  strains for detailed comparisons between genotype and phenotype.    Results  Feature and sequence genome comparisons revealed a high degree of similarity between the three  B. pilosicoli  strains, although the genomes of B2904 and WesB were larger than that of 95/1000 (~2,765, 2.890 and 2.596 Mb, respectively). Genome rearrangements were observed which correlated largely with the positions of mobile genetic elements. Through comparison of the B2904 and WesB genomes with the 95/1000 genome, features that we propose are non-essential due to their absence from 95/1000 include a peptidase, glycine reductase complex components and transposases. Novel bacteriophages were detected in the newly-sequenced genomes, which appeared to have involvement in intra- and inter-species horizontal gene transfer. Phenotypic differences predicted from genome analysis, such as the lack of genes for glucuronate catabolism in 95/1000, were confirmed by phenotyping.    Conclusions  The availability of multiple  B. pilosicoli  genome sequences has allowed us to demonstrate the substantial genomic variation that exists between these strains, and provides an insight into genetic events that are shaping the species. In addition, phenotype screening allowed determination of how genotypic differences translated to phenotype. Further application of such comparisons will improve understanding of the metabolic capabilities of  Brachyspira  species.

bmc genomics

Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity