A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

Bas E. Dutilh; Noriko Cassman; Katelyn McNair; Savannah E. Sanchez; Genivaldo G.Z. Silva; Lance Boling; Jeremy J. Barr; Daan R. Speth; Victor Seguritan; Ramy K. Aziz; Ben Felts; Elizabeth A. Dinsdale; John L. Mokili; Robert A. Edwards

doi:10.1038/ncomms5498

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

Bas E. Dutilh, Noriko Cassman, Katelyn McNair, Savannah E. Sanchez, Genivaldo G.Z. Silva, Lance Boling, Jeremy J. Barr, Daan R. Speth, Victor Seguritan, Ramy K. Aziz, Ben Felts, Elizabeth A. Dinsdale, John L. Mokili, Robert A. Edwards

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Abstract

Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its ∼97kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; it comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all human faecal metagenomic sequencing reads in the public databases. The majority of crAssphage-encoded proteins match no known sequences in the database, which is why it was not detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome.

Original language	English
Article number	4498
Number of pages	11
Journal	Nature Communications
Volume	5
DOIs	https://doi.org/10.1038/ncomms5498
Publication status	Published - 24 Jul 2014
Externally published	Yes

Bibliographical note

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/

Keywords

metagenomics
faecal metagenomes
bacteriophage
metagenomic sequencing

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Dutilh, B. E., Cassman, N., McNair, K., Sanchez, S. E., Silva, G. G. Z., Boling, L., Barr, J. J., Speth, D. R., Seguritan, V., Aziz, R. K., Felts, B., Dinsdale, E. A., Mokili, J. L., & Edwards, R. A. (2014). A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nature Communications, 5, Article 4498. https://doi.org/10.1038/ncomms5498

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abstract = "Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its ∼97kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; it comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all human faecal metagenomic sequencing reads in the public databases. The majority of crAssphage-encoded proteins match no known sequences in the database, which is why it was not detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome.",

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AU - Barr, Jeremy J.

AU - Speth, Daan R.

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N1 - This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/

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N2 - Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its ∼97kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; it comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all human faecal metagenomic sequencing reads in the public databases. The majority of crAssphage-encoded proteins match no known sequences in the database, which is why it was not detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome.

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A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

Abstract

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Keywords

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