Lysogeny is prevalent and widely distributed in the murine gut microbiota
Lysogeny is prevalent and widely distributed in the murine gut microbiota
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DOI：
10.1038/s41396-018-0061-9
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发表时间：
2018-04-01
期刊：
影响因子：
11
通讯作者：
Bae, Jin-Woo
中科院分区：
文献类型：
--
作者：
Kim, Min-Soo;Bae, Jin-Woo
噬菌体是肠道微生物群的核心成员和潜在调节剂；然而，肠道细菌和噬菌体的生态和进化关系尚不清楚。本研究通过检测从共生菌元基因组重构的基因组中的整合前噬菌体，研究了C57BL/6J小鼠细菌群落中溶原菌（lysogenic bacteria, lysogens）的丰度和多样性。对于溶原和噬菌体的活性，我们将噬菌体基因组与游离噬菌体宏基因组进行了比较。在不同分类群中，大多数共生菌被鉴定为溶菌原。在厚壁菌门和变形菌门中发现的溶菌原多于拟杆菌门和放线菌门。原噬菌体基因组与游离噬菌体宏基因组序列相似性较高，表明大多数溶原具有活性，原噬菌体是自发诱导为活性噬菌体的；饮食干预改变了诱导的噬菌体的组成。相比之下，CRISPR-Cas系统存在于很少的共生细菌中，并且很少对肠道噬菌体有活性。细菌-噬菌体感染网络的结构是“嵌套-模块化”的，模块化在不同的分类尺度上出现，表明温带噬菌体特征是在很长的系统发育时间尺度上发展起来的。我们得出结论，噬菌体通才有助于肠道生态系统中溶原性的流行。
Bacteriophages are central members and potential modulators of the gut microbiome; however, the ecological and evolutionary relationships of gut bacteria and phages are poorly understood. Here we investigated the abundance and diversity of lysogenic bacteria (lysogens) in the bacterial community of C57BL/6J mice by detecting integrated prophages in genomes reconstructed from the metagenome of commensal bacteria. For the activities of lysogens and prophages, we compared the prophage genomes with the metagenome of free phages. The majority of commensal bacteria in different taxa were identified as lysogens. More lysogens were found among Firmicutes and Proteobacteria, than among Bacteroidetes and Actinobacteria. The prophage genomes shared high sequence similarity with the metagenome of free phages, indicating that most lysogens appeared to be active, and that prophages are spontaneously induced as active phages; dietary interventions changed the composition of the induced prophages. By contrast, CRISPR-Cas systems were present in few commensal bacteria, and were rarely active against gut phages. The structure of the bacteria-phage infection networks was "nested-modular", with modularity emerging across taxonomic scales, indicating that temperate phage features have developed over a long phylogenetic timescale. We concluded that phage generalists contribute to the prevalence of lysogeny in the gut ecosystem.