Genome binning of viral entities from bulk metagenomics data

Joachim Johansen, Damian R. Plichta, Jakob Nybo Nissen, Marie Louise Jespersen, Shiraz A. Shah, Ling Deng, Jakob Stokholm, Hans Bisgaard, Dennis Sandris Nielsen, Søren J. Sørensen and Simon Rasmussen ()
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Joachim Johansen: University of Copenhagen
Damian R. Plichta: Broad Institute of MIT and Harvard
Jakob Nybo Nissen: University of Copenhagen
Marie Louise Jespersen: University of Copenhagen
Shiraz A. Shah: Herlev and Gentofte Hospital, University of Copenhagen
Ling Deng: University of Copenhagen
Jakob Stokholm: Herlev and Gentofte Hospital, University of Copenhagen
Hans Bisgaard: Herlev and Gentofte Hospital, University of Copenhagen
Dennis Sandris Nielsen: University of Copenhagen
Søren J. Sørensen: University of Copenhagen
Simon Rasmussen: University of Copenhagen

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-28581-5

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