Resurrection of a global, metagenomically defined Gokushovirus

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Data availability
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Abstract

Gokushoviruses are single-stranded, circular DNA bacteriophages found in metagenomic datasets from diverse ecosystems worldwide, including human gut microbiomes. Despite their ubiquity and abundance, little is known about their biology or host range: Isolates are exceedingly rare, known only from three obligate intracellular bacterial genera. By synthesizing circularized phage genomes from prophages embedded in diverse enteric bacteria, we produced gokushoviruses in an experimentally tractable model system, allowing us to investigate their features and biology. We demonstrate that virions can reliably infect and lysogenize hosts by hijacking a conserved chromosome-dimer resolution system. Sequence motifs required for lysogeny are detectable in other metagenomically defined gokushoviruses; however, we show that even partial motifs enable phages to persist cytoplasmically without leading to collapse of their host culture. This ability to employ multiple, disparate survival strategies is likely key to the long-term persistence and global distribution of Gokushovirinae.

Data availability

The data used in this publication (accession numbers, sequences and alignments) are available in the manuscript, its supplementary files and on datadryad.org: https://doi.org/10.5061/dryad.z8w9ghx7s

The following data sets were generated

1. Kirchberger PC
(2020) Resurrection of a Global, Metagenomically Defined Gokushovirus
Dryad Digital Repository, doi.org/10.5061/dryad.z8w9ghx7s.

https://doi.org/10.5061/dryad.z8w9ghx7s

The following previously published data sets were used

1. Moreno-Gallego JL
2. Chou SP
3. Di Rienzi SC
4. Goodrich JK
5. Spector TD
6. Bell JT
7. Youngblut ND
8. Hewson I
9. Reyes A
10. Ley RE
(2019) The virome in adult monozygotic twins with concordant or discordant gut microbiomes
NCBI, PRJEB29491.

https://www.ncbi.nlm.nih.gov/bioproject/PRJEB29491
1. University of Alberta
(2018) metagenomic sequencing of calf gut content-associated microbiota
NCBI, PRJNA362629.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA362629
(2015) A longitudinal analysis of the developing gut microbiome in infants from Finland, Estonia, and Russian Karelia
NCBI, PRJNA290380.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA290380/
1. Ferretti P
2. Pasolli E
3. Tett A
4. Asnicar F
5. Gorfer V
6. Fedi S
7. Armanini F
8. Truong DT
9. Manara S
10. Zolfo M
11. Beghini F
(2016) Mother-infant microbiome vertical transmission
NCBI, PRJNA352475.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA352475
1. Bäckhed F
2. Roswall J
3. Peng Y
4. Feng Q
5. Jia H
6. Kovatcheva-Datchary P
7. Li Y
8. Xia Y
9. Xie H
10. Zhong H
11. Khan MT
(2015) Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
NCBI, PRJEB6456.

https://www.ncbi.nlm.nih.gov/bioproject/285453
1. Stockdale SR
2. Ryan FJ
3. McCann A
4. Dalmasso M
5. Ross PR
6. Hill C
(2018) Viral dark matter in the gut virome of elderly humans
NCBI, PRJNA385126.

https://www.ncbi.nlm.nih.gov/bioproject/385126
1. Feng Q
2. Liang S
3. Jia H
4. Stadlmayr A
5. Tang L
6. Lan Z
7. Zhang D
8. Xia H
9. Xu X
10. Jie Z
11. Su L
(2015) Gut microbiome development along the colorectal adenoma-carcinoma sequence
NCBI, PRJEB7774.

https://www.ncbi.nlm.nih.gov/bioproject/277324
1. Shkoporov A
2. Clooney AG
3. Sutton TD
4. Ryan FJ
5. Daly KM
6. Nolan JA
7. McDonnell SA
8. Khokhlova EV
9. Draper LA
10. Forde A
11. Guerin E
(2019) Longitudinal study of the human gut virome
NCBI, PRJNA545408.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA545408

Article and author information

Author details

Paul C Kirchberger

Department of Integrative Biology, University of Texas at Austin, Austin, United States

For correspondence
pkirchberger@utexas.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-8387-6440
Howard Ochman

Department of Integrative Biology, University of Texas at Austin, Austin, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-1688-7059

Funding

National Institutes of Health (26-1612-1250)

Howard Ochman

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.