Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces

Abstract

Bacteriophages are widely recognised as rapidly evolving biological entities. However, we discovered an ancient genome nearly identical to present-day Mushuvirus mushu, a phage that infects commensal microorganisms in the human gut ecosystem. The DNA damage patterns of this genome have confirmed 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. We also reconstructed and authenticated 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genomes, expanding the known virosphere, and offering new insights into phage-bacteria interactions that cover several millennia.