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

iScience (Aug 2021)

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

Journal volume & issue: Vol. 24, no. 8
p. 102875

Abstract

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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.

Published in iScience

ISSN: 2589-0042 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science
Website: http://www.cell.com/iscience/home

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