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MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies

Author

Listed:
  • Trine Zachariasen

    (Technical University of Denmark)

  • Jakob Russel

    (University of Copenhagen)

  • Charisse Petersen

    (950 West 28th Avenue)

  • Gisle A. Vestergaard

    (Technical University of Denmark)

  • Shiraz Shah

    (University of Copenhagen)

  • Pablo Atienza Lopez

    (Rigshospitalet-Glostrup
    University of Copenhagen)

  • Moschoula Passali

    (Rigshospitalet-Glostrup)

  • Stuart E. Turvey

    (950 West 28th Avenue)

  • Søren J. Sørensen

    (University of Copenhagen)

  • Ole Lund

    (Technical University of Denmark)

  • Jakob Stokholm

    (University of Copenhagen
    University of Copenhagen)

  • Asker Brejnrod

    (Technical University of Denmark)

  • Jonathan Thorsen

    (University of Copenhagen)

Abstract

Metagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurate abundance estimation with functional profiling of assembled genomes. To define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes. Here, we present MAGinator, a freely available tool, tailored for profiling of shotgun metagenomics datasets. MAGinator provides de novo identification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes and genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences.

Suggested Citation

  • Trine Zachariasen & Jakob Russel & Charisse Petersen & Gisle A. Vestergaard & Shiraz Shah & Pablo Atienza Lopez & Moschoula Passali & Stuart E. Turvey & Søren J. Sørensen & Ole Lund & Jakob Stokholm &, 2024. "MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49958-8
    DOI: 10.1038/s41467-024-49958-8
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    References listed on IDEAS

    as
    1. Jakob Stokholm & Martin J. Blaser & Jonathan Thorsen & Morten A. Rasmussen & Johannes Waage & Rebecca K. Vinding & Ann-Marie M. Schoos & Asja Kunøe & Nadia R. Fink & Bo L. Chawes & Klaus Bønnelykke & , 2018. "Maturation of the gut microbiome and risk of asthma in childhood," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    2. Alessio Milanese & Daniel R Mende & Lucas Paoli & Guillem Salazar & Hans-Joachim Ruscheweyh & Miguelangel Cuenca & Pascal Hingamp & Renato Alves & Paul I Costea & Luis Pedro Coelho & Thomas S. B. Schm, 2019. "Microbial abundance, activity and population genomic profiling with mOTUs2," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    3. Jakob Stokholm & Martin J. Blaser & Jonathan Thorsen & Morten A. Rasmussen & Johannes Waage & Rebecca K. Vinding & Ann-Marie M. Schoos & Asja Kunøe & Nadia R. Fink & Bo L. Chawes & Klaus Bønnelykke & , 2018. "Publisher Correction: Maturation of the gut microbiome and risk of asthma in childhood," Nature Communications, Nature, vol. 9(1), pages 1-2, December.
    4. Kirsten M. Ellegaard & Philipp Engel, 2019. "Genomic diversity landscape of the honey bee gut microbiota," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
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