Clades of huge phages from across Earth’s ecosystems
Basem Al-Shayeb, Rohan Sachdeva, Lin-Xing Chen, Fred R. Ward, Patrick Munk, Audra E. Devoto, Cindy J. Castelle, Matthew R. Olm, Keith Bouma‐Gregson, Yuki Amano, Christine He, Raphaël Méheust, Brandon Brooks, Alex D. Thomas, Adi Lavy, Paula B. Matheus Carnevali, Christine Sun, Daniela S. Aliaga Goltsman, Mikayla Borton, Allison Sharrar, Alexander L. Jaffe, Tara Colenbrander Nelson, Rose S. Kantor, Ray Keren, Katherine R. Lane, Ibrahim Farag, Shufei Lei, Kari Finstad, Ronald Amundson, Karthik Anantharaman, Jinglie Zhou, Alexander J. Probst, Mary E. Power, Susannah G. Tringe, Wen‐Jun Li, Kelly Wrighton, Sue Harrison, Michael J. Morowitz, David A. Relman, Jennifer A. Doudna, Anne‐Catherine Lehours, Lesley A. Warren, J.H.D. Cate, Joanne M. Santini, Jillian F. Banfield
Abstract
. 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. Thirty-five genomes were manually curated to completion (circular and no gaps). 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. 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. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. 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. 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.