Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria
Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria
复制标题
生态位特异性的多组学分析为细菌的生态适应提供了新的见解
DOI：
10.1038/ismej.2015.251
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发表时间：
2016
期刊：
影响因子：
11
通讯作者：
Zhou XP
中科院分区：
文献类型：
--
作者：
Zhu B;Ibrahim M;Cui ZQ;Xie GL;Jin GL;Kube M;Li B;Zhou XP
不同的生活方式，从一个saplete到一个病原体，已经在一个物种的细菌中报道过。在这里，我们进行了全基因组调查的生态适应在四个伯克霍尔德氏菌菌株，区分其起源的一部分，土壤或水，但也包括人类和植物病原体的sacetartic微生物群落。结果表明，各菌株在模拟其原始生态位的培养基中通过增加适合度而与其他菌株分离，这与菌株之间代谢能力的差异相对应。此外，菌株特异性代谢和生态位生存通常与基因组变异和相应基因的生态位依赖性差异表达有关。特别是，铁，海藻糖和d-阿拉伯糖醇利用的重要性，突出了参与DNA甲基化和水平基因转移的小生境适应调节相应的操纵子的基础上，我们的多组学数据的综合分析。总的来说，我们的研究结果提供了细菌中生态位特异性适应的见解。
Different lifestyles, ranging from a saprophyte to a pathogen, have been reported in bacteria of one species. Here, we performed genome-wide survey of the ecological adaptation in fourBurkholderia seminalisstrains, distinguished by their origin as part of the saprophytic microbial community of soil or water but also including human and plant pathogens. The results indicated that each strain is separated from the others by increased fitness in medium simulating its original niche corresponding to the difference between strains in metabolic capacities. Furthermore, strain-specific metabolism and niche survival was generally linked with genomic variants and niche-dependent differential expression of the corresponding genes. In particular, the importance of iron, trehalose andd-arabitol utilization was highlighted by the involvement of DNA-methylation and horizontal gene transfer in niche-adapted regulation of the corresponding operons based on the integrated analysis of our multi-omics data. Overall, our results provided insights of niche-specific adaptation in bacteria.