Choi Sukjung, Jin Gwi-Deuk, Park Jongbin, You Inhwan, Kim Eun Bae
Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
Division of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
J Microbiol Biotechnol. 2018 Aug 28;28(8):1352-1359. doi: 10.4014/jmb.1803.03029.
is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of strains via pan-genomic analysis. We compared the genomes of 108 strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (-arabinose, -rhamnose, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restriction-modification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered strains, regardless of habitats.
是一种作为益生菌促进动物肠道健康的乳酸菌，存在于多种栖息地。在此，我们通过泛基因组分析研究了不同菌株簇的基因组特征。我们比较了从NCBI GenBank数据库中获取的108株菌株的基因组。这些基因组大小为2.9 - 3.7 Mbp，G + C含量为44 - 45%。共收集了8847个直系同源基因，并且鉴定出1709个基因作为所有分析菌株的核心基因被共享。基于核心基因的单核苷酸多态性，108株菌株被聚类为五个主要组（G1 - G5），这些组与先前的报道不同，并且与栖息地没有明显关联。对组特异性富集或缺失基因的分析表明，G1和G2富含碳水化合物利用基因（阿拉伯糖、鼠李糖和低聚果糖），而G3、G4和G5拥有更多的限制修饰系统和MazEF毒素 - 抗毒素基因。这些结果表明，无论栖息地如何，在遗传聚类的菌株之间基因含量和生存策略存在关键差异。
