Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
复制标题
DOI：
10.1371/journal.pone.0223680
复制
发表时间：
2019-12-12
期刊：
影响因子：
3.7
通讯作者：
Alm, Eric J.
中科院分区：
文献类型：
--
作者：
Jiang, Xiaofang;Hall, Andrew Brantley;Alm, Eric J.
移动的遗传元件（MGE）驱动肠道微生物组中的广泛水平转移。这种转移可以通过赋予肠道微生物新的代谢能力而有益于人类健康，或者通过将抗生素抗性基因传播给病原体而威胁人类健康。尽管它们具有生物学重要性和医学相关性，但来自肠道微生物组的MGE尚未得到系统表征。在这里，我们提出了一个全面的分析染色体MGE在肠道微生物组中使用的方法，使MGE的可移动单元的识别。我们策划了一个包含5，219个推定MGE的数据库，其中包括七个名为ImmeDB的MGE类。我们观察到，许多MGE携带的基因，可以赋予一个适应性优势的肠道环境，包括基因家族参与抗生素耐药性，胆盐解毒，粘液降解，荚膜多糖生物合成，多糖利用，和孢子形成。我们发现抗生素抗性基因更可能通过整合接合元件或整合可移动元件接合传播，而不是通过原噬菌体转导。MGE的水平转移在门内是广泛的，但在门之间是罕见的，这支持了肠道微生物组中门水平的生态位适应性基因库。ImmeDB将成为未来研究肠道微生物组和MGE社区的宝贵资源。
Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological importance and medical relevance, MGEs from the gut microbiome have not been systematically characterized. Here, we present a comprehensive analysis of chromosomal MGEs in the gut microbiome using a method that enables the identification of the mobilizable unit of MGEs. We curated a database of 5,219 putative MGEs encompassing seven MGE classes called ImmeDB. We observed that many MGEs carry genes that could confer an adaptive advantage to the gut environment including gene families involved in antibiotic resistance, bile salt detoxification, mucus degradation, capsular polysaccharide biosynthesis, polysaccharide utilization, and sporulation. We find that antibiotic resistance genes are more likely to be spread by conjugation via integrative conjugative elements or integrative mobilizable elements than transduction via prophages. Horizontal transfer of MGEs is extensive within phyla but rare across phyla, supporting phylum level niche-adaptive gene pools in the gut microbiome. ImmeDB will be a valuable resource for future studies on the gut microbiome and MGE communities.