Widely used isolation-based methods select against large phage particles, and they can be excluded from phage concentrates obtained by passage through 100-nm or 200-nm filters 1. Most knowledge about phages is based on laboratory-studied examples, the vast majority of which have genomes that are a few tens of kb in length. They spread antibiotic resistance 5 and disperse pathogenicity factors that cause disease in humans and animals 6, 7.
They are agents of ecosystem change because they prey on specific bacterial populations, mediate lateral gene transfer, alter host metabolism and redistribute bacterially derived compounds through cell lysis 2, 3, 4. Phages-viruses that infect bacteria-are considered distinct from cellular life owing to their inability to carry out most biological processes required for reproduction. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems.
We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. Thirty-five genomes were manually curated to completion (circular and no gaps). Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date.
Nature volume 578, pages 425–431 ( 2020) Cite this articleīacteriophages typically have small genomes 1 and depend on their bacterial hosts for replication 2. Clades of huge phages from across Earth’s ecosystems
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