Bacteriophages in ancient human gut metagenomes

Bacteriophages (phages), viruses that infect bacteria, are highly diverse and abundant everywhere on Earth. Recent advances in metagenomic sequencing and computational analysis have made it possible to explore the vast genomic diversity of phages and study their evolution and ecology. However, most studies only sample present-day phages, so they lack a long-term perspective on their evolution. In this study, we present the de novo assembly of 298 ancient phage genomes from publicly available ancient human gut metagenomes dated up to 5300 years before present. We authenticated their ancestral origin based on DNA deamination patterns. Next, we analyzed their relationships to modern viruses from the gastrointestinal tract and predicted hosts with cutting-edge tools. Our analysis revealed ancient representatives of known virus families and genera, as well as ancient phages that were unclassified or only distantly related to known viruses. We also discovered a genome of Mushuvirus mushu, a phage that infects Faecalibacterium prausnitzii, and other commensal bacteria in the human gut ecosystem. Despite 1300 years of evolution on different continents, modern and ancient Mushuvirus genomes share 97.7% nucleotide identity and suggest a long-term mutualistic relationship between the prophage and its host. Overall, our results demonstrate the feasibility of reconstructing high-quality ancient phage genomes and offer new insights into phage-bacteria interactions, expanding our understanding of the virosphere.