PDF(Pubmed)
Abstract：
Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.
摘要：
遗传变异有助于解开噬菌体进化并破译其功能含义。这里,我们探索了肠道基因组中潜在的精细遗传变异，特别是结构变化(SV)。通过在91个人中使用富含病毒的长读宏基因组测序，我们确定了总共14,438个非冗余噬菌体SV,并揭示了它们在人类肠道基因组中的患病率.这些SVs主要富集在参与重组的基因中，DNA甲基化，抗生素耐药性。值得注意的是,大量的噬菌体SV序列与细菌片段具有密切的同源性，与大多数SVs富集水平基因转移（HGT）机制。进一步的研究表明，这些SV序列在特定的噬菌体-细菌对之间进行了遗传交换，特别是在噬菌体和它们各自的细菌宿主之间。温带噬菌体表现出更高的与细菌染色体的遗传交换频率，然后是有毒噬菌体。总的来说，我们的发现为人类肠道基因组的遗传景观提供了见解。
