Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Reading University, Addlestone, Surrey, UK.
BMC Genomics. 2012 Sep 5;13:454. doi: 10.1186/1471-2164-13-454.
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.
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.
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.
厌氧螺旋体短螺旋体引起禽类、猪和人类等动物的肠道疾病。迄今为止，短螺旋体唯一可用的基因组序列是猪分离株 95/1000。在短螺旋体属内的首次种内基因组比较中，我们报告了禽分离株 B. pilosicoli B2904 的全基因组序列、人分离株 B. pilosicoli WesB 的不完全基因组序列以及与 95/1000 的比较。我们还借鉴了其他三个短螺旋体物种的不完全基因组序列。最后，我们报告了高通量 Biolog 表型筛选工具在短螺旋体菌株上的首次应用，用于基因型和表型之间的详细比较。
特征和序列基因组比较显示，三种短螺旋体菌株之间具有高度相似性，尽管 B2904 和 WesB 的基因组大于 95/1000（分别约为 2765、2890 和 2596Mb）。观察到基因组重排，这些重排与移动遗传元件的位置密切相关。通过将 B2904 和 WesB 基因组与 95/1000 基因组进行比较，我们提出由于 95/1000 中不存在，某些特征是非必需的，例如肽酶、甘氨酸还原酶复合物成分和转座酶。在新测序的基因组中检测到新型噬菌体，它们似乎参与了种内和种间的水平基因转移。通过表型分析预测的表型差异，例如 95/1000 中缺乏葡萄糖醛酸代谢基因，通过表型分析得到了证实。
多种短螺旋体基因组序列的可用性使我们能够证明这些菌株之间存在大量基因组变异，并深入了解塑造该物种的遗传事件。此外，表型筛选允许确定基因型差异如何转化为表型。进一步应用这种比较将提高对短螺旋体物种代谢能力的理解。
