Genome binning of viral entities from bulk metagenomics data

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Genome binning of viral entities from bulk metagenomics data. / Johansen, Joachim; Plichta, Damian R.; Nissen, Jakob Nybo; Jespersen, Marie Louise; Shah, Shiraz A.; Deng, Ling; Stokholm, Jakob; Bisgaard, Hans; Nielsen, Dennis Sandris; Sørensen, Søren J.; Rasmussen, Simon.

In: Nature Communications, Vol. 13, 965, 2022.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Johansen, J, Plichta, DR, Nissen, JN, Jespersen, ML, Shah, SA, Deng, L, Stokholm, J, Bisgaard, H, Nielsen, DS, Sørensen, SJ & Rasmussen, S 2022, 'Genome binning of viral entities from bulk metagenomics data', Nature Communications, vol. 13, 965. https://doi.org/10.1038/s41467-022-28581-5

APA

Johansen, J., Plichta, D. R., Nissen, J. N., Jespersen, M. L., Shah, S. A., Deng, L., Stokholm, J., Bisgaard, H., Nielsen, D. S., Sørensen, S. J., & Rasmussen, S. (2022). Genome binning of viral entities from bulk metagenomics data. Nature Communications, 13, [965]. https://doi.org/10.1038/s41467-022-28581-5

Vancouver

Johansen J, Plichta DR, Nissen JN, Jespersen ML, Shah SA, Deng L et al. Genome binning of viral entities from bulk metagenomics data. Nature Communications. 2022;13. 965. https://doi.org/10.1038/s41467-022-28581-5

Author

Johansen, Joachim ; Plichta, Damian R. ; Nissen, Jakob Nybo ; Jespersen, Marie Louise ; Shah, Shiraz A. ; Deng, Ling ; Stokholm, Jakob ; Bisgaard, Hans ; Nielsen, Dennis Sandris ; Sørensen, Søren J. ; Rasmussen, Simon. / Genome binning of viral entities from bulk metagenomics data. In: Nature Communications. 2022 ; Vol. 13.

Bibtex

@article{152f5736d0364501a39222bcd3b18827,
title = "Genome binning of viral entities from bulk metagenomics data",
abstract = "Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.",
author = "Joachim Johansen and Plichta, {Damian R.} and Nissen, {Jakob Nybo} and Jespersen, {Marie Louise} and Shah, {Shiraz A.} and Ling Deng and Jakob Stokholm and Hans Bisgaard and Nielsen, {Dennis Sandris} and S{\o}rensen, {S{\o}ren J.} and Simon Rasmussen",
note = "Publisher Copyright: {\textcopyright} 2022. The Author(s).",
year = "2022",
doi = "10.1038/s41467-022-28581-5",
language = "English",
volume = "13",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - Genome binning of viral entities from bulk metagenomics data

AU - Johansen, Joachim

AU - Plichta, Damian R.

AU - Nissen, Jakob Nybo

AU - Jespersen, Marie Louise

AU - Shah, Shiraz A.

AU - Deng, Ling

AU - Stokholm, Jakob

AU - Bisgaard, Hans

AU - Nielsen, Dennis Sandris

AU - Sørensen, Søren J.

AU - Rasmussen, Simon

N1 - Publisher Copyright: © 2022. The Author(s).

PY - 2022

Y1 - 2022

N2 - Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.

AB - Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.

U2 - 10.1038/s41467-022-28581-5

DO - 10.1038/s41467-022-28581-5

M3 - Journal article

C2 - 35181661

AN - SCOPUS:85124932686

VL - 13

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 965

ER -

ID: 298733406