ΦCrAss001 Represents the Most Abundant Bacteriophage Family in the Human Gut and Infects Bacteroides Intestinalis

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Nov 16

PMID 30429469

Citations 155

Authors

Andrey N Shkoporov

Ekaterina V Khokhlova

C Brian Fitzgerald

Stephen R Stockdale

Lorraine A Draper

R Paul Ross

Colin Hill

Affiliations

Soon will be listed here.

Abstract

CrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales. Despite being found in ~50% of individuals and representing up to 90% of human gut viromes, members of this viral family have never been isolated in culture and remain understudied. Here, we report the isolation of a CrAssphage (ΦCrAss001) from human faecal material. This bacteriophage infects the human gut symbiont Bacteroides intestinalis, confirming previous in silico predictions of the likely host. DNA sequencing demonstrates that the bacteriophage genome is circular, 102 kb in size, and has unusual structural traits. In addition, electron microscopy confirms that ΦcrAss001 has a podovirus-like morphology. Despite the absence of obvious lysogeny genes, ΦcrAss001 replicates in a way that does not disrupt proliferation of the host bacterium, and is able to maintain itself in continuous host culture during several weeks.

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References

Reyes A, Blanton L, Cao S, Zhao G, Manary M, Trehan I . Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proc Natl Acad Sci U S A. 2015; 112(38):11941-6. PMC: 4586842. DOI: 10.1073/pnas.1514285112. View

Soding J, Biegert A, Lupas A . The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005; 33(Web Server issue):W244-8. PMC: 1160169. DOI: 10.1093/nar/gki408. View

Nurk S, Meleshko D, Korobeynikov A, Pevzner P . metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017; 27(5):824-834. PMC: 5411777. DOI: 10.1101/gr.213959.116. View

Garneau J, Depardieu F, Fortier L, Bikard D, Monot M . PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci Rep. 2017; 7(1):8292. PMC: 5557969. DOI: 10.1038/s41598-017-07910-5. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Duncan S, Hold G, Harmsen H, Stewart C, Flint H . Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol. 2003; 52(Pt 6):2141-2146. DOI: 10.1099/00207713-52-6-2141. View

Aggarwala V, Liang G, Bushman F . Viral communities of the human gut: metagenomic analysis of composition and dynamics. Mob DNA. 2017; 8:12. PMC: 5627405. DOI: 10.1186/s13100-017-0095-y. View

De Sordi L, Khanna V, Debarbieux L . The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses. Cell Host Microbe. 2017; 22(6):801-808.e3. DOI: 10.1016/j.chom.2017.10.010. View

Novacek J, Siborova M, Benesik M, Pantucek R, Doskar J, Plevka P . Structure and genome release of Twort-like Myoviridae phage with a double-layered baseplate. Proc Natl Acad Sci U S A. 2016; 113(33):9351-6. PMC: 4995954. DOI: 10.1073/pnas.1605883113. View

10.

Shkoporov A, Ryan F, Draper L, Forde A, Stockdale S, Daly K . Reproducible protocols for metagenomic analysis of human faecal phageomes. Microbiome. 2018; 6(1):68. PMC: 5892011. DOI: 10.1186/s40168-018-0446-z. View

11.

Zimmermann L, Stephens A, Nam S, Rau D, Kubler J, Lozajic M . A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. J Mol Biol. 2017; 430(15):2237-2243. DOI: 10.1016/j.jmb.2017.12.007. View

12.

Knowles B, Silveira C, Bailey B, Barott K, Cantu V, Cobian-Guemes A . Lytic to temperate switching of viral communities. Nature. 2016; 531(7595):466-70. DOI: 10.1038/nature17193. View

13.

Minot S, Bryson A, Chehoud C, Wu G, Lewis J, Bushman F . Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A. 2013; 110(30):12450-5. PMC: 3725073. DOI: 10.1073/pnas.1300833110. View

14.

Yarygin K, Tyakht A, Larin A, Kostryukova E, Kolchenko S, Bitner V . Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses. PLoS One. 2017; 12(4):e0176154. PMC: 5407692. DOI: 10.1371/journal.pone.0176154. View

15.

Avrani S, Schwartz D, Lindell D . Virus-host swinging party in the oceans: Incorporating biological complexity into paradigms of antagonistic coexistence. Mob Genet Elements. 2012; 2(2):88-95. PMC: 3429526. DOI: 10.4161/mge.20031. View

16.

Holmfeldt K, Solonenko N, Shah M, Corrier K, Riemann L, VerBerkmoes N . Twelve previously unknown phage genera are ubiquitous in global oceans. Proc Natl Acad Sci U S A. 2013; 110(31):12798-803. PMC: 3732932. DOI: 10.1073/pnas.1305956110. View

17.

Guerin E, Shkoporov A, Stockdale S, Clooney A, Ryan F, Sutton T . Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut. Cell Host Microbe. 2018; 24(5):653-664.e6. DOI: 10.1016/j.chom.2018.10.002. View

18.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

19.

Barr J, Auro R, Furlan M, Whiteson K, Erb M, Pogliano J . Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A. 2013; 110(26):10771-6. PMC: 3696810. DOI: 10.1073/pnas.1305923110. View

20.

Siringan P, Connerton P, Cummings N, Connerton I . Alternative bacteriophage life cycles: the carrier state of Campylobacter jejuni. Open Biol. 2014; 4:130200. PMC: 3971406. DOI: 10.1098/rsob.130200. View