Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna Street, 20-704, Lublin, Poland.
Genomed SA, 12 Ponczowa Street, 02-971, Warsaw, Poland.
Sci Rep. 2020 Feb 6;10(1):1986. doi: 10.1038/s41598-020-58929-0.
Enterobacter aerogenes LU2 was isolated from cow rumen and recognized as a potential succinic acid producer in our previous study. Here, we present the first complete genome sequence of this new, wild strain and report its basic genetic features from a biotechnological perspective. The MinION single-molecule nanopore sequencer supported by the Illumina MiSeq platform yielded a circular 5,062,651 bp chromosome with a GC content of 55% that lacked plasmids. A total of 4,986 genes, including 4,741 protein-coding genes, 22 rRNA-, 86 tRNA-, and 10 ncRNA-encoding genes and 127 pseudogenes, were predicted. The genome features of the studied strain and other Enterobacteriaceae strains were compared. Functional studies on the genome content, metabolic pathways, growth, and carbon transport and utilization were performed. The genomic analysis indicates that succinic acid can be produced by the LU2 strain through the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. Antibiotic resistance genes were determined, and the potential for bacteriocin production was verified. Furthermore, one intact prophage region of length ~31,9 kb, 47 genomic islands (GIs) and many insertion sequences (ISs) as well as tandem repeats (TRs) were identified. No clustered regularly interspaced short palindromic repeats (CRISPRs) were found. Finally, comparative genome analysis with well-known succinic acid producers was conducted. The genome sequence illustrates that the LU2 strain has several desirable traits, which confirm its potential to be a highly efficient platform for the production of bulk chemicals.
从奶牛瘤胃中分离到的产气肠杆菌 LU2 是我们之前研究中潜在的琥珀酸生产菌。在此，我们首次报道了该新野生菌株的完整基因组序列，并从生物技术角度报告了其基本遗传特征。Illumina MiSeq 平台支持的 MinION 单分子纳米孔测序仪生成了一个圆形的 5062651bp 染色体，GC 含量为 55%，不含质粒。共预测到 4986 个基因，包括 4741 个蛋白编码基因、22 个 rRNA、86 个 tRNA 和 10 个 ncRNA 编码基因以及 127 个假基因。比较了研究菌株和其他肠杆菌科菌株的基因组特征。对基因组内容、代谢途径、生长以及碳运输和利用进行了功能研究。基因组分析表明，LU2 菌株可以通过三羧酸循环（TCA）的还原分支和乙醛酸途径来生产琥珀酸。确定了抗生素抗性基因，并验证了细菌素产生的潜力。此外，鉴定出一个完整的长度约为 319kb 的原噬菌体区域、47 个基因组岛（GIs）和许多插入序列（ISs）以及串联重复（TRs）。未发现成簇的规律间隔短回文重复序列（CRISPRs）。最后，与知名琥珀酸生产菌进行了比较基因组分析。基因组序列表明，LU2 菌株具有一些理想的特性，这证实了其作为高效生产大宗化学品平台的潜力。
