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- Title
Genome binning of viral entities from bulk metagenomics data.
- Authors
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
- 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. Here, Johansen et al. develop an approach, Phages from Metagenomics Binning (PHAMB), 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, unveiling viral-microbial host interactions in the gut.
- Subjects
METAGENOMICS; ECOSYSTEM dynamics; HUMAN microbiota; VIRAL genomes; SHOTGUN sequencing; GASTROINTESTINAL system; GENOMES
- Publication
Nature Communications, 2022, Vol 13, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-022-28581-5