Genome binning of viral entities from bulk metagenomics data

Research output: Contribution to journalJournal articleResearchpeer-review


  • Fulltext

    Final published version, 2.2 MB, PDF document

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.

Original languageEnglish
Article number965
JournalNature Communications
Number of pages12
Publication statusPublished - 2022

Bibliographical note

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

Number of downloads are based on statistics from Google Scholar and

No data available

ID: 298733406