Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland.
Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland.
Nat Commun. 2024 Jan 23;15(1):495. doi: 10.1038/s41467-023-44370-0.
Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.
噬菌体被广泛认为是快速进化的生物实体。然而，关于古代噬菌体的知识有限。在这里，我们分析了先前从古代粪便和人类肠道内容物样本中生成的 DNA 序列数据集，并鉴定出一个与现代 Mushuvirus mushu 几乎相同的古老噬菌体基因组，Mushuvirus mushu 是一种感染肠道共生细菌的病毒。该基因组的 DNA 损伤模式与其古老起源一致，尽管经历了 1300 年的进化，古老的 Mushuvirus 基因组与现代对应物仍有 97.7%的核苷酸同一性，这表明噬菌体与其宿主之间存在长期关系。此外，我们从过去 5300 年中重建和验证了 297 个其他噬菌体基因组，包括属于未知家族的基因组。我们的研究结果表明，重建古代噬菌体基因组序列是可行的，从而扩大了已知的病毒圈，并深入了解了跨越数千年的噬菌体-细菌相互作用。
