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首页> 外文期刊>Journal of Biotechnology >Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data
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Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data

机译：从原始基因组数据推断出益生菌大肠杆菌Nissle 1917编码序列的基因组特殊性和代谢潜力

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Probiotic Escherichia coli strain Nissle 1917 (O6:K5:H1) is a commensal E. coli isolate that has a long tradition in medicine for the treatment of various intestinal disorders in humans. To elucidate the molecular basis of its probiotic nature, we started sequencing the genome of this organism with a whole-genome shotgun approach. A 7.8-fold coverage of the genomic sequence has been generated and is now in the finishing stage. To exploit the genome data as early as possible and to generate hypotheses for functional studies, the unfinished sequencing data were analyzed in this work using a new method [Sun, J., Zeng, A.P., 2004. IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics 5, 112] which is particularly suitable for the prediction of coding sequences (CDSs) from unannotated genome sequence. The CDSs predicted for E. coli Nissle 1917 were compared with those of all five other sequenced E. coli strains (E. coli K-12 MG1655, E. coli K-12 W3110, E. coli CFT073, EHEC O157:H7 EDL933 and EHEC O157:H7 Sakai) published to date. Five thousand one hundred and ninety-two CDSs were predicted for E. coli Nissle 1917, of which 1065 were assigned with enzyme EC numbers. The comparison of all predicted CDSs of E. coli Nissle 1917 to the other E. coli strains revealed 108 CDSs specific for this isolate. They are organized as four big genome islands and many other smaller gene clusters. Based on CDSs with EC numbers for enzymes, the potential metabolic network of Nissle 1917 was reconstructed and compared to those of the other five E. coli strains. Overall, the comparative genomic analysis sheds light on the genomic peculiarity of the probiotic E. coli strain Nissle 1917 and is helpful for designing further functional studies long before the sequencing project is completely finished.
机译：益生大肠埃希氏菌菌株Nissle 1917（O6：K5：H1）是一种常见的大肠杆菌分离株，在治疗人类各种肠道疾病的医学上具有悠久的传统。为了阐明其益生菌性质的分子基础，我们开始使用全基因组shot弹枪方法对该生物的基因组进行测序。已经产生了7.8倍的基因组序列覆盖率，目前处于完成阶段。为了尽早开发基因组数据并生成功能研究假设，本工作中使用了一种新方法对未完成的测序数据进行了分析[Sun，J.，Zeng，AP，2004。直接从无注释的低覆盖率细菌基因组序列进行计算机重建代谢网络。 [BMC Bioinformatics 5，112]，它特别适用于根据未注释的基因组序列预测编码序列（CDS）。将针对大肠杆菌Nissle 1917预测的CDS与所有其他五种测序的大肠杆菌菌株（E. coli K-12 MG1655，E。coli K-12 W3110，E。coli CFT073，EHEC O157：H7 EDL933和EHEC O157：H7 Sakai）至今已发布。 1917年的大肠杆菌Nissle预测有592个CDS，其中1065个具有EC编号。将大肠杆菌Nissle 1917的所有预测CDS与其他大肠杆菌菌株进行比较，发现该分离株具有108种CDS。它们被组织成四个大的基因组岛和许多其他较小的基因簇。基于带有酶EC编号的CDS，重建了Nissle 1917的潜在代谢网络，并将其与其他五种大肠杆菌菌株的代谢网络进行了比较。总体而言，比较基因组分析揭示了益生菌大肠杆菌Nissle 1917菌株的基因组特殊性，有助于在测序项目完全完成之前进行进一步的功能研究。

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