Closely related Lak megaphages replicate in the microbiomes of diverse animals
Marco A. Crisci,
Lin-Xing Chen,
Audra E. Devoto,
Adair L. Borges,
Nicola Bordin,
Rohan Sachdeva,
Adrian Tett,
Allison M. Sharrar,
Nicola Segata,
Francesco Debenedetti,
Mick Bailey,
Rachel Burt,
Rhiannon M. Wood,
Lewis J. Rowden,
Paula M. Corsini,
Steven van Winden,
Mark A. Holmes,
Shufei Lei,
Jillian F. Banfield,
Joanne M. Santini
Affiliations
Marco A. Crisci
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
Lin-Xing Chen
Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
Audra E. Devoto
Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
Adair L. Borges
Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
Nicola Bordin
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
Rohan Sachdeva
Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
Adrian Tett
Department CIBIO, University of Trento, Trento, Italy
Allison M. Sharrar
Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
Nicola Segata
Department CIBIO, University of Trento, Trento, Italy
Francesco Debenedetti
Bristol Veterinary School, University of Bristol, Langford, Bristol, UK
Mick Bailey
Bristol Veterinary School, University of Bristol, Langford, Bristol, UK
Rachel Burt
Bristol Veterinary School, University of Bristol, Langford, Bristol, UK
Rhiannon M. Wood
Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
Lewis J. Rowden
Zoological Society of London, London, UK
Paula M. Corsini
Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
Steven van Winden
Royal Veterinary College, London, UK
Mark A. Holmes
Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
Shufei Lei
Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
Jillian F. Banfield
Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA; The University of Melbourne, Melbourne, VIC, Australia; Corresponding author
Joanne M. Santini
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK; Corresponding author
Summary: Lak phages with alternatively coded ∼540 kbp genomes were recently reported to replicate in Prevotella in microbiomes of humans that consume a non-Western diet, baboons, and pigs. Here, we explore Lak phage diversity and broader distribution using diagnostic polymerase chain reaction and genome-resolved metagenomics. Lak phages were detected in 13 animal types, including reptiles, and are particularly prevalent in pigs. Tracking Lak through the pig gastrointestinal tract revealed significant enrichment in the hindgut compared to the foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. An anomalously large (∼660 kbp) complete genome reconstructed for the most deeply branched Lak from a horse microbiome is also alternatively coded. From the Lak genomes, we identified proteins associated with specific animal species; notably, most have no functional predictions. The presence of closely related Lak phages in diverse animals indicates facile distribution coupled to host-specific adaptation.
