The plasticity of bacterial and archaeal genomes makes examining their ecological and evolutionary dynamics both exciting and challenging. The same mechanisms that enable rapid genomic change and adaptation confound current approaches for recovering complete genomes from metagenomes. Here, we use strain-specific patterns of DNA methylation to resolve complex bacterial genomes from the long-read metagenome of a marine microbial consortia, the 'pink berries' of the Sippewissett Marsh. Unique combinations of restriction-modification (RM) systems encoded by the bacteria produced distinctive methylation profiles that accurately binned and classified metagenomic sequences. We linked the methylation patterns of each metagenome-assembled genome with encoded DNA methyltransferases and discovered new restriction modification (RM) defense systems, including novel associations of RM systems with RNase toxins. Using this approach, we finished the largest and most complex circularized bacterial genome ever recovered from a metagenome (7.9 Mb with >600 IS elements), the finished genome of Thiohalocapsa sp. PB-PSB1 the dominant bacteria in the consortia. From these methylation-binned genomes, we identified instances of lateral gene transfer between sulfur-cycling symbionts (Thiohalocapsa sp. PB-PSB1 and Desulfofustis sp. PB-SRB1), phage infection, and strain-level structural variation.

中文翻译：

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元基因组甲基化模式可解析复杂的微生物基因组

细菌和古细菌基因组的可塑性使得检查其生态和进化动力学既令人兴奋又充满挑战。能够快速进行基因组改变和适应的相同机制混淆了目前用于从元基因组中恢复完整基因组的方法。在这里，我们使用DNA甲基化的特定菌株模式，从海洋微生物群落（Sippewissett Marsh的“粉红色浆果”）的长期读取的基因组中解析复杂的细菌基因组。由细菌编码的限制性修饰（RM）系统的独特组合产生了独特的甲基化谱，可以准确地对宏基因组序列进行分类和分类。我们将每个元基因组组装基因组的甲基化模式与编码的DNA甲基转移酶相关联，并发现了新的限制性修饰（RM）防御系统，包括RM系统与RNase毒素的新型关联。使用这种方法，我们完成了有史以来最大的，最复杂的环状细菌基因组测序，该细菌基因组是从超基因组（7.9兆比特，具有> 600个IS元素）中回收的，该基因组是Thiohalocapsa sp。PB-PSB1是联盟中的优势细菌。从这些甲基化结合的基因组中，我们确定了硫循环共生体（硫代硫菌种PB-PSB1和脱硫果蝇种PB-SRB1），噬菌体感染和菌株水平结构变异之间的横向基因转移实例。